diff --git a/bibserver/parser.py b/bibserver/parser.py index d36bb8bb..9140a845 100644 --- a/bibserver/parser.py +++ b/bibserver/parser.py @@ -3,6 +3,7 @@ from parsers.BibTexParser import BibTexParser from parsers.JSONParser import JSONParser from parsers.CSVParser import CSVParser +from parsers.RISParser import RISParser class Parser(object): @@ -13,17 +14,16 @@ def parse(self, fileobj, format): :return: a python dict json-i-fiable to bibjson. ''' if format == "bibtex" or format == "bib": - parser = BibTexParser() - data, metadata = parser.parse(fileobj) + parser = BibTexParser(fileobj) elif format == "json": - parser = JSONParser() - data, metadata = parser.parse(fileobj) + parser = JSONParser(fileobj) elif format == "csv" or format == "google": - parser = CSVParser() - data, metadata = parser.parse(fileobj) + parser = CSVParser(fileobj) + elif format == "ris": + parser = RISParser(fileobj) else: raise Exception('Unable to convert from format: %s' % format) - + data, metadata = parser.parse() return data, metadata diff --git a/bibserver/parsers/BibTexParser.py b/bibserver/parsers/BibTexParser.py index 4975e0ae..071f4f7c 100644 --- a/bibserver/parsers/BibTexParser.py +++ b/bibserver/parsers/BibTexParser.py @@ -4,6 +4,8 @@ import unicodedata import re +from bibserver.parsers import BaseParser + '''this file can be called as a module or called directly from the command line like so: python BibTexParser.py /path/to/file.bib @@ -23,9 +25,11 @@ Returns a record dict ''' -class BibTexParser(object): +class BibTexParser(BaseParser): - def __init__(self): + def __init__(self, fileobj): + super(BibTexParser, self).__init__(fileobj) + # set which bibjson schema this parser parses to self.schema = "v0.82" self.has_metadata = False @@ -46,13 +50,13 @@ def __init__(self): } self.identifier_types = ["doi","isbn","issn"] - def parse(self, fileobj): + def parse(self): '''given a fileobject, parse it for bibtex records, and pass them to the record parser''' records = [] record = "" # read each line, bundle them up until they form an object, then send for parsing - for line in fileobj: + for line in self.fileobj: if '--BREAK--' in line: break else: @@ -2663,11 +2667,10 @@ def getnames(self,names): # in case file is run directly if __name__ == "__main__": - import sys - parser = BibTexParser() + import sys try: - fileobj = open(sys.argv[1]) - print parser.parse(fileobj) + parser = BibTexParser(open(sys.argv[1])) + print parser.parse() except: print parser.parse_record(sys.argv[1]) diff --git a/bibserver/parsers/CSVParser.py b/bibserver/parsers/CSVParser.py index 96f96530..d7439fe3 100644 --- a/bibserver/parsers/CSVParser.py +++ b/bibserver/parsers/CSVParser.py @@ -1,13 +1,11 @@ import csv +from bibserver.parsers import BaseParser -class CSVParser(object): +class CSVParser(BaseParser): - def __init__(self): - pass - - def parse(self, fileobj): + def parse(self): #dialect = csv.Sniffer().sniff(fileobj.read(1024)) - d = csv.DictReader(fileobj) + d = csv.DictReader(self.fileobj) data = [] # do any required conversions diff --git a/bibserver/parsers/JSONParser.py b/bibserver/parsers/JSONParser.py index 4be4152f..8fea4d25 100644 --- a/bibserver/parsers/JSONParser.py +++ b/bibserver/parsers/JSONParser.py @@ -1,12 +1,10 @@ import json +from bibserver.parsers import BaseParser -class JSONParser(object): +class JSONParser(BaseParser): - def __init__(self): - pass - - def parse(self, fileobj): - incoming = json.load(fileobj) + def parse(self): + incoming = json.load(self.fileobj) if 'records' in incoming: # if the incoming is bibjson, get records and metadata diff --git a/bibserver/parsers/RISParser.py b/bibserver/parsers/RISParser.py new file mode 100644 index 00000000..8b0b3a4d --- /dev/null +++ b/bibserver/parsers/RISParser.py @@ -0,0 +1,109 @@ +'''this file can be called as a module or called directly from the command line like so: + +python RISParser.py /path/to/file.txt +Returns a list of record dicts + +Details of the RIS format +http://en.wikipedia.org/wiki/RIS_%28file_format%29 +''' + +FIELD_MAP = { + "DO": "doi", + "SP": "pages", + "M2": "start page", + "DB": "name of database", + "DA": "date", + "M1": "number", + "M3": "type", + "N1": "notes", + "ST": "short title", + "DP": "database provider", + "CN": "call number", + "IS": "number", + "LB": "label", + "TA": "translated author", + "TY": "type ", + "UR": "url", + "TT": "translated title", + "PY": "year", + "PB": "publisher", + "A3": "tertiary author", + "C8": "custom 8", + "A4": "subsidiary author", + "TI": "title", + "C3": "custom 3", + "C2": "pmcid", + "C1": "note", + "C7": "custom 7", + "C6": "nihmsid", + "C5": "custom 5", + "C4": "custom 4", + "AB": "note", + "AD": "institution", + "VL": "volume", + "CA": "caption", + "T2": "secondary title", + "T3": "tertiary title", + "AN": "accession number", + "L4": "figure", + "NV": "number of volumes", + "AU": "author", + "RP": "reprint edition", + "L1": "file attachments", + "ET": "epub date", + "A2": "author", + "RN": "notes", + "LA": "language", + "CY": "place published", + "J2": "alternate title", + "RI": "reviewed item", + "KW": "keywords", + "SN": "issn", + "Y2": "access date", + "SE": "section", + "OP": "original publication" +} + +VALUE_MAP = { + 'AU' : lambda v: [{u'name':vv.decode('utf8')} for vv in v] +} +DEFAULT_VALUE_FUNC = lambda v: u' '.join(vv.decode('utf8') for vv in v) + +from bibserver.parsers import BaseParser + +class RISParser(BaseParser): + def __init__(self, fileobj): + super(RISParser, self).__init__(fileobj) + self.data = [] + + def add_chunk(self, chunk): + if not chunk: return + tmp = {} + for k,v in chunk.items(): + tmp[FIELD_MAP.get(k, k)] = VALUE_MAP.get(k, DEFAULT_VALUE_FUNC)(v) + self.data.append(tmp) + + def parse(self): + data, chunk = [], {} + for line in self.fileobj: + line = line.strip() + if not line: continue + parts = line.split(' - ') + if len(parts) < 2: continue + field = parts[0] + if field == 'TY': + self.add_chunk(chunk) + chunk = {} + value = ' - '.join(parts[1:]) + if value: + chunk.setdefault(field, []).append(value) + self.add_chunk(chunk) + return self.data, {} + +# in case file is run directly +if __name__ == "__main__": + import sys, json + fileobj = open(sys.argv[1]) + parser = RISParser(fileobj) + data, metadata = parser.parse() + sys.stdout.write(json.dumps(data, indent=2)) diff --git a/bibserver/parsers/__init__.py b/bibserver/parsers/__init__.py index e69de29b..2db15779 100644 --- a/bibserver/parsers/__init__.py +++ b/bibserver/parsers/__init__.py @@ -0,0 +1,8 @@ +class BaseParser(object): + def __init__(self, fileobj): + if hasattr(fileobj, 'seek'): + # Some files have Byte-order marks inserted at the start + possible_BOM = fileobj.read(3) + if possible_BOM != '\xef\xbb\xbf': + fileobj.seek(0) + self.fileobj = fileobj \ No newline at end of file diff --git a/doc/Makefile b/doc/Makefile new file mode 100644 index 00000000..bfe25628 --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make ' where is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/BibServer.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/BibServer.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/BibServer" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/BibServer" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/doc/conf.py b/doc/conf.py new file mode 100644 index 00000000..1a57ec52 --- /dev/null +++ b/doc/conf.py @@ -0,0 +1,242 @@ +# -*- coding: utf-8 -*- +# +# BibServer documentation build configuration file, created by +# sphinx-quickstart on Thu Jan 19 10:39:35 2012. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'BibServer' +copyright = u'2012, Open Knowledge Foundation' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '1.0' +# The full version, including alpha/beta/rc tags. +release = '1.0' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'BibServerdoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'BibServer.tex', u'BibServer Documentation', + u'Open Knowledge Foundation', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'bibserver', u'BibServer Documentation', + [u'Open Knowledge Foundation'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'BibServer', u'BibServer Documentation', + u'Open Knowledge Foundation', 'BibServer', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 00000000..d071aea2 --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,18 @@ +==================================== +Welcome to BibServer's documentation +==================================== + +Contents: + +.. toctree:: + :maxdepth: 2 + + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/test/data/sample.ris b/test/data/sample.ris new file mode 100644 index 00000000..cdf2c347 --- /dev/null +++ b/test/data/sample.ris @@ -0,0 +1,3683 @@ +TY - JOUR +AU - Kolluru, B.K. +AU - Hawizy, L. +AU - Murray Rust, P. +AU - Tsujii, J. +AU - Ananiadou, S. +PY - 2011 +TI - Using Workflows to Explore and Optimise Named Entity Recognition for Chemisty +SP - e20181 +JF - PloS ONE +VL - 6 +IS - 5 +N1 - open access +N1 - Using Workflows to Explore and Optimise Named Entity Recognition for Chemisty +N1 - Murray Rust +M3 - doi: 10.1371/journal/pone.0020181 +UR - http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020181 +ID - 267 +ER - + +TY - JOUR +AU - Paton, R. S. +AU - Goodman, J. M. +AU - Pellegrinet, S. C. +PY - 2009 +TI - Mechanistic Insights into the Catalytic Asymmetric Allylboration of Ketones: Brønsted or Lewis Acid Activation? +SP - 37-40 +JF - Org. Lett. +VL - 11 +N1 - Mechanistic Insights into the Catalytic Asymmetric Allylboration of Ketones: Brønsted or Lewis Acid Activation? +N1 - Goodman +M3 - DOI: 10.1021/ol802270u +ID - 263 +ER - + +TY - JOUR +AU - Nigsch, F. +AU - Macaluso, N.J.M. +AU - Mitchell, J.B.O. +AU - Zmuidinavicius, D. +PY - 2009 +TI - Computational Toxicology: An Overview of the Sources of Data and of Modelling Methods +SP - 1-14 +JF - Expert Opinion on Drug Metabolism and Toxicology +VL - 5 +N1 - Computational Toxicology: An Overview of the Sources of Data and of Modelling Methods +N1 - Mitchell +ID - 261 +ER - + +TY - JOUR +AU - Holliday, G.L. +AU - Mitchell, J.B.O. +AU - Thornton, J.M. +PY - 2009 +TI - Understanding the functional roles of amino acid residues in enzyme catalysis +SP - 560-577 +JF - J. of Mol. Bio. +VL - 390 +N1 - Understanding the functional roles of amino acid residues in enzyme catalysis +M3 - doi: 10.1016/j.jmb.2009.05.015 +PMID 19447117 +N2 - The MACiE database contains 223 distinct step-wise enzyme reaction mechanisms and holds representatives from each EC sub-subclass where there is a crystal structure and sufficient evidence in the literature to support a mechanism. Each catalytic step of every reaction sequence in MACiE is fully annotated so that it includes the function of the catalytic residues involved in the reaction and the mechanism by which substrates are transformed into products. Using MACiE as a knowledge base, we have seen that the top 10 most catalytic residues are histidine, aspartate, glutamate, lysine, cysteine, arginine, serine, threonine, tyrosine and tryptophan. Of these only seven (cysteine, histidine, aspartate, lysine, serine, threonine and tyrosine) dominate catalysis and provide essentially five functional roles that are essential. Stabilisation is the most common and essential role for all classes of enzyme, followed by general acid/base (proton acceptor and proton donor) functionality, with nucleophilic addition following closely behind (nucleophile and nucleofuge). We investigated the occurrence of these residues in MACiE and the Catalytic Site Atlas and found that, as expected, certain residue types are associated with each functional role, with some residue types able to perform diverse roles. In addition, it was seen that different EC classes of enzyme have a tendency to employ different residues for catalysis. Further, we show that whilst the differences between EC classes in catalytic residue composition are not immediately obvious from the general classes of Ingold mechanisms, there is some weak correlation between the mechanisms involved in a given EC class and the functions that the catalytic amino acid residues are performing. The analysis presented here provides a valuable insight into the functional roles of catalytic amino acid residues, which may have applications in many aspects of enzymology, from the design of novel enzymes to the prediction and validation of enzyme reaction mechanisms. +ID - 266 +ER - + +TY - JOUR +AU - Fedorov, M. V. +AU - Goodman, J. M. +AU - Schumm, S. +PY - 2009 +TI - The effect of sodium chloride on poly-L-glutamate conformation +JF - Chem. Commun. +VL - article in press +N1 - The effect of sodium chloride on poly-L-glutamate conformation +N1 - Goodman +M3 - (DOI: 10.1039/b816055d) +ID - 264 +ER - + +TY - JOUR +AU - Blomberg, L.M. +AU - Mangold, M. +AU - Mitchell, J.B.O. +AU - Blumberger, J. +PY - 2009 +TI - Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase +JF - J. Chem. Theory Comput. +N1 - Article ASAP +N1 - Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase +N1 - Mitchell +M3 - doi: 10.1021/ct800480d +ID - 262 +ER - + +TY - JOUR +AU - Blomberg, L. M. +AU - Mangold, M. +AU - Mitchell, J. B. O. +AU - Blumberger, J. +PY - 2009 +TI - Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase +JF - J. Chem. Theory Comput. +VL - ASAP Article +N1 - Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase +N1 - Mitchell +M3 - (DOI: 10.1021/ct800480d) +ID - 265 +ER - + +TY - JOUR +AU - Nigsch, F. +AU - Mitchell, J.B.O. +PY - 2008 +TI - How to Winnow Actives from Inactives: Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow +JF - Journal of Chemical Information and Modelling +N1 - ASAP article +N1 - How to Winnow Actives from Inactives: Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow +N1 - doi.org/10.1021/ci700350n +N1 - Mitchell +UR - http://dx.doi.org/10.1021/ci700350n>doi:10.1021/ci700350n +ID - 257 +ER - + +TY - JOUR +AU - Nigsch, F +AU - A Bender +AU - Jenkins, JL +AU - Mitchell, JBO +PY - 2008 +TI - Ligand-Target Prediction using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics +SP - 2313-2325 +JF - J. Chem. Inf. Model +VL - 48 +N1 - Ligand-Target Prediction using Winnow and Naive Bayesian Algorithms and the Implications of Overall Performance Statistics +N1 - Mitchell +ID - 260 +ER - + +TY - JOUR +AU - Hughes, L.D. +AU - Palmer, D.S. +AU - Nigsch, F. +AU - Mitchell, J.B.O. +PY - 2008 +TI - Why Are Some Properties More Difficult To Predict than Others? A Study of QSPR Models of Solubility, Melting Point, and Log P +SP - 220-232 +JF - Journal of Chemical Information and Modeling +VL - 48 +N1 - ASAP +N1 - Why Are Some Properties More Difficult To Predict than Others? A Study of QSPR Models of Solubility, Melting Point, and Log P +N1 - doi: 10.1021/ci700307p +N1 - Mitchell +UR - http://dx.doi.org/10.1021/ci700307p +ID - 256 +ER - + +TY - JOUR +AU - Buis, N. +AU - Skylaris, C-K +AU - Grant, G. H. +AU - Rajendra, E. +AU - Payne, M. C. +AU - Venkitaraman, A. R. +PY - 2008 +TI - Classical molecular dynamics simulations of the complex between the RAD51 protein and the BRC hairpin loops of the BRCA2 protein +SP - 749 — 759 +JF - Molecular Simulation +VL - 34 +IS - 8 +N1 - Classical molecular dynamics simulations of the complex between the RAD51 protein and the BRC hairpin loops of the BRCA2 protein +N1 - Grant +M3 - DOI: 10.1080/08927020802213281 +UR - http://dx.doi.org/10.1080/08927020802213281 +ID - 258 +ER - + +TY - JOUR +AU - Banham, J.E. +AU - Baker, C.M. +AU - Ceola, S. +AU - Day, I.J. +AU - Grant, G.H. +AU - Groenen, J.J. +AU - Rodgers, C.T. +AU - Jeschke, G. +AU - Timmel, C.R. +PY - 2008 +TI - Distance measurements in the borderline region of applicability +of CW EPR and DEER: A model study on a homologous series +of spin-labelled peptides +SP - 202-218 +JF - J. of Magnetic Resonance +VL - 191 +N1 - Distance measurements in the borderline region of applicability +of CW EPR and DEER: A model study on a homologous series +of spin-labelled peptides +N1 - Grant +ID - 259 +ER - + +TY - JOUR +AU - Torrance, J.W. +AU - Holliday, G.L. +AU - Mitchell, J.B.O. +AU - Thornton, J.M. +PY - 2007 +TI - The Geometry of Interactions Between Catalytic Residues and their Substrates +SP - 1140-1152 +JF - Journal of Molecular Biology +VL - 369 +N1 - The Geometry of Interactions Between Catalytic Residues and their Substrates +N1 - Mitchell +N1 - DOI: 10.1016/j.jmb.2007.03.055 +UR - +ID - 227 +ER - + +TY - CONF +AU - Rupp, C.J. +AU - Copestake, A. +AU - Corbett, P. +AU - Waldron, B. +PY - 2007 +TI - Integrating General-Purpose and Domain-Specific +Components in the Analysis of Scientific Text. +BT - All-Hands 2007 +N1 - Integrating General-Purpose and Domain-Specific +Components in the Analysis of Scientific Text. +N1 - Murray Rust +ID - 247 +ER - + +TY - JOUR +AU - Paton, R. S. +AU - Goodman, J. M. +PY - 2007 +TI - Enantioselectivity in the boron aldol reactions of methyl ketones +SP - 2124-2126. +JF - Chem. Commun. +N1 - Advance article +N1 - Enantioselectivity in the boron aldol reactions of methyl ketones +N1 - DOI: 10.1039/b704786j +N1 - Goodman +ID - 217 +ER - + +TY - JOUR +AU - Palmer, D.S. +AU - O'Boyle, N.M. +AU - Glen, R.C. +AU - Mitchell, J.B.O. +PY - 2007 +TI - Random Forest Models to Predict Aqueous Solubility +SP - 150-158 +JF - J. Chem. Inf. Model +VL - 47 +IS - 1 +N1 - ASAP Article +N1 - Random Forest Models to Predict Aqueous Solubility +N1 - DOI: 10.1021/ci060164k +N1 - Mitchell, Glen +UR - http://pubs.acs.org/cgi-bin/abstract.cgi/jcisd8/asap/abs/ci060164k.html +http://dx.doi.org/10.1021/ci060164k +ID - 206 +ER - + +TY - JOUR +AU - O'Boyle, N.M. +AU - Holliday, G.L. +AU - Almonacid, D.E. +AU - Mitchell, J.B.O. +PY - 2007 +TI - Using Reaction Mechanism to Measure Enzyme Similarity +SP - 1484-1499 +JF - Journal of Molecular Biology +VL - 368 +N1 - Using Reaction Mechanism to Measure Enzyme Similarity +N1 - Mitchell +N1 - DOI: 10.1016/j.jmb.2007.02.065 +UR - +ID - 228 +ER - + +TY - JOUR +AU - Nigsch, F. +AU - Klaffke, W. +AU - Miret, S. +PY - 2007 +TI - In Vitro Models For Intestinal Absorption +JF - Expert Opinion on Drug Metabolism and Toxicology +VL - accepted +N1 - In Vitro Models For Intestinal Absorption +ID - 242 +ER - + +TY - JOUR +AU - Nigsch, F. +AU - Klaffke, W. +AU - Miret, S. +PY - 2007 +TI - In Vitro Models For Processes Involved In Intestinal Absorption + + +SP - 545-556 +JF - Expert Opinion on Drug Metabolism and Toxicology, +VL - 3 +IS - (4) +N1 - In Vitro Models For Processes Involved In Intestinal Absorption + + +N1 - DOI: 10.1517/17425225.3.4.545 +N1 - Mitchell +UR - http://dx.doi.org/10.1517/17425225.3.4.545 +ID - 252 +ER - + +TY - JOUR +AU - Matamala, A. R. +AU - Almonacid, D.E. +AU - Figueroa, M.F. +AU - Martínez-Oyanedel, J. +AU - M.C. Bunster +PY - 2007 +TI - A Semiempirical Approach to the Intra-Phycocyanin and Inter-Phycocyanin Fluorescence Resonance Energy-Transfer Pathways in Phycobilisomes. +SP - 1200-1207 +JF - J. Comp. Chemistry +VL - 28 +N1 - A Semiempirical Approach to the Intra-Phycocyanin and Inter-Phycocyanin Fluorescence Resonance Energy-Transfer Pathways in Phycobilisomes. +N1 - DOI: 10.1002/jcc.20628 +N1 - Mitchell +UR - http://dx.doi.org/10.1002/jcc.20628 +ID - 230 +ER - + +TY - JOUR +AU - Luzanov, A. V. +AU - Nerukh, D. +PY - 2007 +TI - Simple One-Electron Invariants of Molecular Chirality +SP - 417-435 +JF - J. Math. Chem +IS - 41 +N1 - Simple One-Electron Invariants of Molecular Chirality +UR - http://www.springerlink.com/content/e2163855026458t1/?p=dbb1637f20e04e1185d4c54e35174b20&pi=6&hl=u>417-435 +ID - 240 +ER - + +TY - JOUR +AU - Lunn, J. C. +AU - Kuhnle, G. +AU - Mai, V. +AU - Frankenfeld, C. +AU - Shuker, D. E. G. +AU - Glen, R. C. +AU - Goodman, J. M. +AU - Pollock, J. R. A. +AU - Bingham, S. A. +PY - 2007 +TI - The effect of haem in red and processed meat on the endogenous formation of N-nitroso compounds in the upper gastrointestinal tract +SP - 685-690 +JF - Carcinogenesis +VL - 28 +N1 - The effect of haem in red and processed meat on the endogenous formation of N-nitroso compounds in the upper gastrointestinal tract +N1 - DOI: 10.1093/carcin/bgl192 +N1 - Goodman +Glen +ID - 221 +ER - + +TY - JOUR +AU - Llinàs, A. +AU - Burley, J. C. +AU - Box, K. J. +AU - Glen, R. C. +AU - Goodman, J. M. +PY - 2007 +TI - Diclofenac Solubility: Independent Determination of the Intrinsic Solubility of Three Crystal Forms +SP - 979-983 +JF - J. Med. Chem. +VL - 50 +N1 - Diclofenac Solubility: Independent Determination of the Intrinsic Solubility of Three Crystal Forms +N1 - DOI: 10.1021/jm0612970 +N1 - Goodman +Glen +ID - 219 +ER - + +TY - JOUR +AU - Llinàs, A. +AU - Box, K. J. +AU - Burley, J. C. +AU - Glen, R. C. +AU - Goodman, J. M. +PY - 2007 +TI - A new method for the reproducible generation of polymorphs: two forms of sulindac with very different solubilities +SP - 379-381 +JF - J. Appl. Cryst. +VL - 40 +N1 - A new method for the reproducible generation of polymorphs: two forms of sulindac with very different solubilities +N1 - DOI: 10.1107/S0021889807007832 +N1 - Goodman +Glen +ID - 218 +ER - + +TY - JOUR +AU - Kirtay, C.K. +AU - Mitchell, J.B.O. +AU - Lumley, J.A. +PY - 2007 +TI - Scoring Functions and Enrichment: A Case Study on Hsp90 +SP - 27 +N1 - 26-JAN-07 +JF - BMC Bioinformatics +VL - 8 +N1 - Scoring Functions and Enrichment: A Case Study on Hsp90 +N1 - DOI: 10.1186/1471-2105-8-27 +N1 - Mitchell +UR - http://dx.doi.org/10.1186/1471-2105-8-27 +http://www.biomedcentral.com/1471-2105/8/27/abstract +ID - 203 +ER - + +TY - JOUR +AU - Holliday, G.L. +AU - Almonacid, D.E. +AU - Mitchell, J.B.O. +AU - Thornton, J.M. +PY - 2007 +TI - The Chemistry of Protein Catalysis +SP - 1261-1277 +JF - Journal of Molecular Biology +VL - 372 +N1 - The Chemistry of Protein Catalysis +N1 - DOI: 10.1016/j.jmb.2007.07.034 +N1 - Mitchell +UR - http://dx.doi.org/10.1016/j.jmb.2007.07.034 +ID - 253 +ER - + +TY - JOUR +AU - Holliday, G.L. +AU - Almonacid, D.E. +AU - Bartlett, G.J. +AU - O'Boyle, N.M. +AU - Torrance, J.W. +AU - Murray-Rust, P. +AU - Mitchell, J.B.O. +AU - J.M. Thornton +PY - 2007 +TI - MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms +SP - D515-D520 +JF - Nucleic Acids Research +VL - 35 +SN - DOI: 10.1093/nar/gkl774 +N1 - MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms +N1 - Mitchell +Murray Rust +ID - 215 +ER - + +TY - JOUR +AU - Goodman, J. M. +AU - Socorro, I. M. +PY - 2007 +TI - Computational assessment of synthetic procedures +SP - 351-357. +JF - J. Comp.-Aided Molecular Design +VL - 21 +N1 - Computational assessment of synthetic procedures +N1 - DOI: 10.1007/s10822-007-9120-4 +N1 - Goodman +ID - 248 +ER - + +TY - JOUR +AU - Fedorov, M V +AU - Goodman, J M +AU - Schumm, S +PY - 2007 +TI - Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an /in silico/ study +SP - 5423 - 5435 +JF - J. Phys. Chem. +VL - 9 +N1 - Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an /in silico/ study +N1 - DOI: 10.1039/b706564g +N1 - Goodman +ID - 254 +ER - + +TY - JOUR +AU - Fedorov, M. V. +AU - Flad, J. J. +AU - Chuev, G. N. +AU - Grasedyck, L. +AU - Khoromskij, B. N. +PY - 2007 +TI - A structured low-rank wavelet solver for the Ornstein-Zernike integral equation +SP - 47-73 +N1 - May, 2007 +JF - Computing +VL - 80 +IS - 1 +SN - 0010-485X (Print) 1436-5057 (Online) +N1 - A structured low-rank wavelet solver for the Ornstein-Zernike integral equation +N1 - Goodman +N1 - DOI 10.1007/s00607-007-0221-7 +UR - http://www.springerlink.com/content/103076/ +ID - 223 +ER - + +TY - JOUR +AU - Fedorov, M. V. +AU - Kornyshev, A. A. +PY - 2007 +TI - Unravelling the solvent response to neutral and charged solutes +SP - 1-16 +N1 - 10-JAN-2007 +JF - J. Mol. Phys. +VL - 105 +IS - (1) +N1 - Unravelling the solvent response to neutral and charged solutes +N1 - Goodman +ID - 232 +ER - + +TY - JOUR +AU - Duer, M. J. +AU - Garcia, F. +AU - Goodman, J. M. +AU - Hehn, J. P. +AU - Kowenicki, R. A. +AU - Naseri, V. +AU - McPartlin, M. +AU - Stead, M. L. +AU - Stein, R. +AU - Wright, D. S. +PY - 2007 +TI - Structural, Solid-State NMR and Theoretical Studies of the Inverse Coordination of Lithium Chloride Using Group 13 Phosphide Hosts +SP - 1251-1260 +JF - Chem. Eur. J. +VL - 13 +N1 - Structural, Solid-State NMR and Theoretical Studies of the Inverse Coordination of Lithium Chloride Using Group 13 Phosphide Hosts +N1 - DOI: 10.1002/chem.200600781 +N1 - Goodman +ID - 220 +ER - + +TY - CONF +AU - Corbett, P. +AU - C.Batchelor; +AU - Teufel, S. +PY - 2007 +TI - Annotation of Chemical Named Entities +BT - BioNLP 2007: Biological, translational, and clinical language +processing +CY - Prague +SP - 57–64 +N1 - Annotation of Chemical Named Entities +N1 - Murray Rust +ID - 246 +ER - + +TY - JOUR +AU - Contreras-Martel, C. +AU - Matamala, A. +AU - Bruna, C. +AU - Poo-Caamaño, G. +AU - Almonacid, D. +AU - Figueroa, M. +AU - Martínez-Oyanedel, J. +AU - Bunster, M. +PY - 2007 +TI - The structure at 2 A resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC-PC complex +SP - 388-396 +JF - Biophysical Chem. +VL - 125 +N1 - The structure at 2 A resolution of Phycocyanin from Gracilaria chilensis and the energy transfer network in a PC-PC complex +N1 - DOI: 10.1016/j.bpc.2006.09.014 +N1 - Mitchell +UR - http://dx.doi.org/10.1016/j.bpc.2006.09.014 +ID - 231 +ER - + +TY - JOUR +AU - Chiodo, S. +AU - Chuev, G. N. +AU - Erofeeva, S. E. +AU - Fedorov, M. V. +AU - Russo, N. +AU - Sicilia, E. +PY - 2007 +TI - Comparative study of electrostatic solvent response by RISM and PCM methods +SP - 265-274 +N1 - FEB-07 +JF - Inter. J. Quantum Chem. +VL - 107 +IS - (2) +N1 - Comparative study of electrostatic solvent response by RISM and PCM methods +N1 - Goodman +ID - 233 +ER - + +TY - JOUR +AU - Cannon, E.O. +AU - Amini, A. +AU - Bender, A. +AU - Sternberg, M.J.E. +AU - Muggleton, S.H. +AU - Glen, R.C. +AU - Mitchell, J.B.O. +PY - 2007 +TI - Support Vector Inductive Logic Programming Outperforms the Naive Bayes Classifier and Inductive Logic Programming for the Classification of Bioactive Chemical Compounds +SP - 269-280 +JF - J. Comp-Aided Mol. Design +VL - 21 +N1 - Support Vector Inductive Logic Programming Outperforms the Naive Bayes Classifier and Inductive Logic Programming for the Classification of Bioactive Chemical Compounds +N1 - DOI: 10.1007/s10822-007-9113-3 +N1 - Mitchell +UR - http://dx.doi.org/10.1007/s10822-007-9113-3 +ID - 229 +ER - + +TY - JOUR +AU - Boyer, S. +AU - Arnby, C. H. +AU - Carlsson, L. +AU - Smith, J. +AU - Stein, V. +AU - Glen, R. C. +PY - 2007 +TI - Reaction Site Mapping of Xenobiotic Biotransformations. +SP - 583-590. +JF - J. of Chemical Information and Modeling +VL - 47 +IS - (2) +N1 - Reaction Site Mapping of Xenobiotic Biotransformations. +N1 - Glen +ID - 251 +ER - + +TY - JOUR +AU - Bellesia, G. +AU - Fedorov, M. V. +AU - Timoshenko, E. G. +PY - 2007 +TI - Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides +SP - 455-476 +N1 - 1-JAN-2007 +JF - Physica a-Statistical Mechanics & its applications +VL - 373 +N1 - Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides +N1 - Goodman +UR - http://apps.isiknowledge.com/WoS/CIW.cgi?SID=R2kHjg@oiEPG1jn6njM&Func=Links;ServiceName=TransferToWoS;PointOfEntry=FullRecord;request_from=UML;UT=000242316000039 +ID - 234 +ER - + +TY - CONF +AU - Batchelor, C.R. +AU - Corbett, P.T. +PY - 2007 +TI - Semantic enrichment of journal articles using chemical named entity +recognition +BT - Proceedings of the ACL 2007 Demo and Poster Sessions +CY - Prague +SP - 45–48 +N1 - Semantic enrichment of journal articles using chemical named entity +recognition +ID - 245 +ER - + +TY - JOUR +AU - Baker, C.M. +AU - Grant, G.H. +PY - 2007 +TI - Modelling Aromatic Liquids: Toluene, Phenol and Pyridine +SP - 530-548 +JF - J. Chem. Theory. Comp. +VL - 3 +N1 - Modelling Aromatic Liquids: Toluene, Phenol and Pyridine +N1 - Grant +ID - 225 +ER - + +TY - JOUR +AU - Baker, C.M. +AU - Grant, G.H. +PY - 2007 +TI - The role of aromatic interactions in nucleic acid recognition +SP - 456-470 +JF - Biopolymers +VL - 85 +N1 - The role of aromatic interactions in nucleic acid recognition +N1 - Grant +ID - 224 +ER - + +TY - JOUR +AU - Baker, C.M. +AU - G.H.Grant +PY - 2007 +TI - The role of solvent in the conformational equilibrium and solution dynamics of Amino-phenylethanol +JF - J.Phys. Chem. B +IS - in press (June 2007) +N1 - The role of solvent in the conformational equilibrium and solution dynamics of Amino-phenylethanol +N1 - Grant +ID - 226 +ER - + +TY - JOUR +AU - Adams, N. +AU - Schubert, U. S. +PY - 2007 +TI - Poly(2-oxazolines) in biological and biomedical application contexts +SP - 1504-1520 +JF - Advanced Drug Delivery Reviews +VL - 59 +N1 - Poly(2-oxazolines) in biological and biomedical application contexts +N1 - Murray Rust +ID - 255 +ER - + +TY - JOUR +AU - Socorro, I M +AU - Goodman, J M +PY - 2006 +TI - The ROBIA program for predicting organic reactivity +SP - 606-614 +JF - J. Chem. Inf. Model. +VL - 46 +IS - (2) +N1 - The ROBIA program for predicting organic reactivity +N1 - DOI: 10.1021/ci050379e +N1 - Goodman +UR - DOI: 10.1021/ci050379e +ID - 196 +ER - + +TY - JOUR +AU - Rodgers, S. +AU - Glen, R. C. +AU - Bender, A. +PY - 2006 +TI - Characterising Bitterness: Identification of Key Structural Features and Development of a Classification Model +SP - 569 - 576 +JF - J. Chem. Inf. Model +VL - 46 +IS - (2) +SN - 1549-9596 +N1 - Characterising Bitterness: Identification of Key Structural Features and Development of a Classification Model +N1 - Glen +N1 - http://dx.doi.org/10.1021/ci0504418 +ID - 195 +ER - + +TY - JOUR +AU - Pellegrinet, S. C. +AU - Goodman, J. M. +PY - 2006 +TI - Asymmetric Conjugate Addition of Alkynylboronates to Enones: Rationale for the Intriguing Catalysis Exerted by Binaphthols +SP - 3116 - 3117 +JF - J. Am. Chem. Soc. +VL - 128 +N1 - Asymmetric Conjugate Addition of Alkynylboronates to Enones: Rationale for the Intriguing Catalysis Exerted by Binaphthols +N1 - DOI: 10.1021/ja056727a +N1 - Goodman +ID - 222 +ER - + +TY - JOUR +AU - Paton, R. S. +AU - Goodman, J. M. +PY - 2006 +TI - Understanding the Origins of Remote Asymmetric Induction in the Boron Aldol Reactions of beta-Alkoxy Methyl Ketones +SP - 4299-4302. +JF - Org. Lett. +VL - 8 +N1 - Understanding the Origins of Remote Asymmetric Induction in the Boron Aldol Reactions of beta-Alkoxy Methyl Ketones +N1 - DOI: 10.1021/ol061671q +N1 - Goodman +ID - 212 +ER - + +TY - JOUR +AU - O'Boyle, N.M. +AU - Holliday, G.L. +AU - Almonacid, D.E. +AU - Mitchell, J.B.O. +PY - 2006 +TI - Using Reaction Mechanism to Measure Enzyme Similarity +JF - Journal of Molecular Biology +VL - submitted +N1 - Using Reaction Mechanism to Measure Enzyme Similarity +N1 - +Mitchelll +ID - 204 +ER - + +TY - JOUR +AU - Nigsch, F. +AU - Bender, A. +AU - Buuren, B. van +AU - Tissen, J. +AU - Nigsch, E. +AU - Mitchell, J.B.O. +PY - 2006 +TI - Melting Point Prediction Employing k-nearest Neighbor Algorithms and Genetic Parameter Optimization +SP - 2412-2422 +JF - Journal of Chemical Information and Modeling +VL - 46 +IS - DOI: 10.1021/ci060149f +N1 - ASAP +N1 - Melting Point Prediction Employing k-nearest Neighbor Algorithms and Genetic Parameter Optimization +N1 - Mitchell +ID - 197 +ER - + +TY - JOUR +AU - Moses, J. E. +AU - Commeiras, L. +AU - Adlington, R. M. +AU - Baldwin, J. E. +AU - Baker, Christopher +AU - Grant, G.H. +PY - 2006 +TI - Biomimetic synthesis of the ubiquitin activating enzyme E1 inhibitor, (+)-panepophenanthrin +SP - 9892–9901 +JF - Tetrahedron +VL - 62 +N1 - Biomimetic synthesis of the ubiquitin activating enzyme E1 inhibitor, (+)-panepophenanthrin +N1 - Grant +ID - 210 +ER - + +TY - JOUR +AU - Llinas, A. +AU - Fabian, L. +AU - Burley, J. C. +AU - Streek, J. van de +AU - Goodman, J. M. +PY - 2006 +TI - Amodiaquinium dichloride dihydrate from laboratory powder diffraction data +SP - o4196-o4199. +JF - Acta Cryst. +VL - E 2006 +IS - 62 +N1 - Amodiaquinium dichloride dihydrate from laboratory powder diffraction data +N1 - DOI: 10.1107/S1600536806033691 +N1 - Goodman +ID - 205 +ER - + +TY - JOUR +AU - Khechinashvili, N. N. +AU - Fedorov, M. V. +AU - Kabanov, A. V. +AU - Monti, S. +AU - Ghio, C. +AU - Soda, K. +PY - 2006 +TI - Side chain dynamics and alternative hydrogen bonding in the mechanism of protein thermostabilization +SP - 255-262 +N1 - DEC-2006 +JF - J. Biomol. Structure & Dynamics +VL - 24 +IS - (3) +N1 - Side chain dynamics and alternative hydrogen bonding in the mechanism of protein thermostabilization +N1 - Goodman +UR - http://apps.isiknowledge.com/WoS/CIW.cgi?SID=W225EhI6oe9Oh9kdc@m&Func=OneClickSearch&field=AU&val=Soda+K&ut=000242412800007&auloc=6&fullauth=%20%28Soda,%20K.%29&curr_doc=1/5&Form=FullRecordPage&doc=1/5 +ID - 236 +ER - + +TY - JOUR +AU - Karthikeyan, M. +AU - Bender, A. +PY - 2006 +TI - Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme +SP - 452 - 461 +JF - J. Chem. Inf. Model. +VL - 46 +IS - 2 +SN - 1549-9596 +N1 - Harvesting Chemical Information from the Internet Using a Distributed Approach: ChemXtreme +N1 - Glen +N1 - http://dx.doi.org/10.1021/ci050329+ +ID - 194 +ER - + +TY - JOUR +AU - Holliday, G. L. +AU - Murray-Rust, P. +AU - H. S. Rzepa +PY - 2006 +TI - Chemical Markup, XML and the Worldwide Web. Part 6. CMLReact; An XML Vocabulary for Chemical Reactions +SP - 145-157 +JF - J. Chem. Inf. Mod. +VL - 46 +N1 - Chemical Markup, XML and the Worldwide Web. Part 6. CMLReact; An XML Vocabulary for Chemical Reactions +N1 - Murray-Rust +Mitchell +ID - 185 +ER - + +TY - JOUR +AU - Holliday, G.L. +AU - Almonacid, D.E. +AU - Bartlett, G.J. +AU - O'Boyle, N.M. +AU - Torrance, J.W. +AU - Murray-Rust, P. +AU - Mitchell, J.B.O. +AU - Thornton, J.M. +PY - 2006 +TI - MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms +JF - Nucleic Acids Research +VL - Advance Access Online + +IS - DOI: 10.1093/nar/gkl774 +N1 - MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms +N1 - Mitchell +Murray Rust +N2 - +UR - http://nar.oxfordjournals.org/cgi/content/abstract/gkl774>MACiE +ID - 201 +ER - + +TY - JOUR +AU - Goodman, S. C. PellegrinetJ. M. +PY - 2006 +TI - Asymmetric Conjugate Addition of Alkynylboronates to Enones: Rationale for the Intriguing Catalysis Exerted by Binaphthols +SP - 3116-3117 +JF - J. Am. Chem. Soc. +VL - 128 +N1 - Asymmetric Conjugate Addition of Alkynylboronates to Enones: Rationale for the Intriguing Catalysis Exerted by Binaphthols +N1 - Goodman +N1 - DOI: 10.1021/ja056727a +ID - 214 +ER - + +TY - JOUR +AU - Glen, R C +AU - Bender, A +AU - Arnby, C A +AU - Carlsson, L +AU - Boyer, S +AU - Smith, J +PY - 2006 +TI - Circular fingrprints: Flexible molecular descriptors with applications from physical chemistry to ADME +SP - 199-204 +JF - IDrugs +VL - 9 +IS - 3 +SN - 1369-7056 +N1 - Circular fingrprints: Flexible molecular descriptors with applications from physical chemistry to ADME +N1 - Glen +ID - 193 +ER - + +TY - JOUR +AU - Fedorov, M. V. +AU - Schumm, S. +AU - Goodman, J. M. +PY - 2006 +TI - Solvent Effects and Conformational Stability of a Tripeptide +SP - 141-149. +JF - Lecture Notes in Bioinformatics +VL - 4216 +N1 - Solvent Effects and Conformational Stability of a Tripeptide +N1 - DOI: 10.1007/11875741_14 +N1 - Goodman +N1 - CompLife 2006, +ID - 213 +ER - + +TY - JOUR +AU - Cusson, M. +AU - Béliveau, C. +AU - Sen, S. E. +AU - Vandermoten, S. +AU - Francis, F. +AU - Haubruge, E. +AU - Rehse, P. +AU - Huggins, D.J. +AU - Grant, G.H. +PY - 2006 +TI - Unique features of lepidopteran farnesyl diphosphate synthase: implications for the biosynthesis of ethyl-substituted juvenile hormones +SP - 742–758 +JF - Proteins +VL - 65 +N1 - Unique features of lepidopteran farnesyl diphosphate synthase: implications for the biosynthesis of ethyl-substituted juvenile hormones +N1 - Grant +ID - 209 +ER - + +TY - CONF +AU - Corbett, P. +AU - Murray-Rust, P. +PY - 2006 +TI - High-throughput identification of chemistry in life science texts +BT - CompLife 2006 +CY - Cambridge, UK +VL - Proceedings of Computational Life Sciences +SP - LNBI 4216:107-118, +N1 - High-throughput identification of chemistry in life science texts +ID - 239 +ER - + +TY - CONF +AU - Copestake, A. +AU - Corbett, P. +AU - Murray-Rust, P. +AU - Rupp, C. J. +AU - Siddharthan, A. +AU - S.Teufel +AU - Waldron, B. +PY - 2006 +TI - An Architecture for Language Processing for Scientific Texts +BT - All Hands Meeting 2006 (AHM2006) +CY - Nottingham, UK +PB - Proceedings of the UK e-Science Programme +N1 - An Architecture for Language Processing for Scientific Texts +N1 - Murray Rust +ID - 238 +ER - + +TY - JOUR +AU - Chuev, G. N. +AU - Chiodo, S. +AU - Erofeeva, S. E. +AU - Fedorov, M. V. +AU - Russo, N. +AU - Sicilia, E. +PY - 2006 +TI - A quasilinear RISM approach for the computation of solvation free energy of ionic species +SP - 485-489 +N1 - 6-FEB-2006 +JF - Chem. Phys. Letts +VL - 418 +IS - (4-6) +N1 - A quasilinear RISM approach for the computation of solvation free energy of ionic species +N1 - Goodman +UR - http://apps.isiknowledge.com/WoS/CIW.cgi?SID=R2kHjg@oiEPG1jn6njM&Func=Links;ServiceName=TransferToWoS;PointOfEntry=FullRecord;request_from=UML;UT=000235104200038 +ID - 237 +ER - + +TY - JOUR +AU - Cannon, E.O. +AU - Bender, A. +AU - Palmer, D.S. +AU - Mitchell, J.B.O. +PY - 2006 +TI - Chemoinformatics-based Classification of Prohibited Substances Employed for Doping in Sport +SP - 2369-2380 +JF - Journal of Chemical Information and Modeling +VL - 46 +IS - DOI: 10.1021/ci0601160 +N1 - ASAP +N1 - Chemoinformatics-based Classification of Prohibited Substances Employed for Doping in Sport +N1 - Mitchell +UR - DOI: 10.1021/ci0601160 +ID - 198 +ER - + +TY - JOUR +AU - Cannon, E.O. +AU - Mitchell, J.B.O. +PY - 2006 +TI - Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint +SP - 173-182 +JF - Lecture Notes in Bioinformatics +VL - 4216 +N1 - Classifying the World Anti-Doping Agency's 2005 Prohibited List Using the Chemistry Development Kit Fingerprint +N1 - Mitchell +ID - 199 +ER - + +TY - JOUR +AU - Bender, A. +AU - Fergus, S. +AU - Galloway, W. R. J. D. +AU - Glansdorp, F. G. +AU - Marsden, D. M. +AU - Nicholson, R. L. +AU - Spandl, R. J. +AU - Thomas, G. L. +AU - Wyatt, E. E. +AU - Glen, R. C. +AU - Spring, D. R. +PY - 2006 +TI - Diversity Oriented Synthesis: A Challenge for Synthetic Chemists +SP - 47 - 60 +JF - Ernst Schering Res. Found. Workshop. +VL - (58) +N1 - Diversity Oriented Synthesis: A Challenge for Synthetic Chemists +N1 - Glen +ID - 158 +ER - + +TY - JOUR +AU - Baker, C.M. +AU - Grant, G.H. +PY - 2006 +TI - A solvent induced mechanism for conformational change +SP - 1387–1389 +JF - Chem. Comm. +N1 - A solvent induced mechanism for conformational change +N1 - Grant +ID - 208 +ER - + +TY - JOUR +AU - Baker, C.M. +AU - Grant, G.H. +PY - 2006 +TI - The Structure of Aromatic Liquids +JF - J.Chem. Theory. Comp. +VL - in press +N1 - The Structure of Aromatic Liquids +ID - 211 +ER - + +TY - JOUR +AU - Baker, C.M. +AU - Grant, G.H. +PY - 2006 +TI - The Structure of Liquid Benzene +SP - 947–955 +JF - J.Chem. Theory. Comp. +VL - 2 +N1 - The Structure of Liquid Benzene +N1 - Grant +ID - 207 +ER - + +TY - CONF +AU - White, T O +AU - Bruin, R P +AU - Wakelin, J +AU - Chapman, C +AU - Osborn, D +AU - Murray-Rust, P +AU - Artacho, E +AU - Dove, M T +AU - Calleja, M +PY - 2005 +TI - eScience methods for the combinatorial chemistry problem of adsorption of pollutant organic molecules on mineral surfaces +BT - Proceedings of the UK e-Science All Hands Meeting +VL - 424 +N1 - eScience methods for the combinatorial chemistry problem of adsorption of pollutant organic molecules on mineral surfaces +N1 - Murray-Rust +ID - 189 +ER - + +TY - JOUR +AU - Wakelin, J. +AU - Murray-Rust, P. +AU - Tyrrell, S. +AU - Y. Zhang +AU - H.S. Rzepa +AU - Garcia, A +PY - 2005 +TI - CML Tools and Information Flow in Atomic Scale Simulations +SP - 315-322. +JF - Mol. Simulations +VL - 31 +N1 - CML Tools and Information Flow in Atomic Scale Simulations +N1 - Murray-Rust +ID - 181 +ER - + +TY - CONF +AU - Townsend, J +AU - Copestake, A +AU - Murray-Rust, P +AU - Teufel, S +AU - Waudby, C +PY - 2005 +TI - Language Technology for Processing Chemistry Publications +BT - Proceedings of the UK e-Science All Hands Meeting +VL - 467 +N1 - Language Technology for Processing Chemistry Publications +N1 - Murray-Rust +ID - 188 +ER - + +TY - JOUR +AU - Socorro, I. M. +AU - Taylor, K. +AU - Goodman, J. M. +PY - 2005 +TI - ROBIA: A Reaction Prediction Program +SP - 3541-3544 +JF - Org. Lett. +VL - 7 +N1 - ROBIA: A Reaction Prediction Program +N1 - Goodman +ID - 176 +ER - + +TY - JOUR +AU - Silva, M. A. +AU - Goodman, J. M. +PY - 2005 +TI - Aziridinium ring opening: a simple ionic reaction pathway with sequential transition states +SP - 2067-2069 +JF - Tetrahedron Letters +VL - 46 +N1 - Aziridinium ring opening: a simple ionic reaction pathway with sequential transition states +N1 - DOI: 10.1016/j.tetlet.2005.01.142 +N1 - Goodman +ID - 178 +ER - + +TY - JOUR +AU - Silva, K. M. de +AU - Goodman, J. M. +PY - 2005 +TI - What is the smallest saturated acyclic alkane that cannot be made? +SP - 81-87 +JF - J. Chem. Inf. Model. +VL - 45 +N1 - What is the smallest saturated acyclic alkane that cannot be made? +N1 - DOI: 10.1021/ci0497657 +N1 - Goodman +N1 - Highlighted in Most-Accessed Articles January-June, 2005 +ID - 24 +ER - + +TY - JOUR +AU - Rilee, M +AU - Curtis, S A +AU - Dorband, J E +AU - Cheung, C Y +AU - LeMoigne, J J. +AU - Lary, D E +AU - Mussa, H Y +PY - 2005 +TI - Working notes on a developmental approach to autonomous spacecraft and the recovery of the Hubble Space Telescope, +N1 - March 21, 2005 +JF - The AAAI Symposium Series +N1 - Working notes on a developmental approach to autonomous spacecraft and the recovery of the Hubble Space Telescope, +N1 - Glen +ID - 180 +ER - + +TY - JOUR +AU - Pellegrinet, S. C. +AU - Silva, M. A. +AU - Goodman, J. M. +PY - 2005 +TI - Computational evaluation of asymmetric Diels-Alder reactions of vinylboranes with chiral dienes +SP - 2461-2464. +JF - Tetrahedron Letters +VL - 46 +N1 - Computational evaluation of asymmetric Diels-Alder reactions of vinylboranes with chiral dienes +N1 - DOI: 10.1016/j.tetlet.2005.02.050 +N1 - Goodman +ID - 164 +ER - + +TY - JOUR +AU - Paterson, I. +AU - Menche, D. +AU - Britton, R. +AU - Hakansson, A. E. +AU - Silva-Martinez, M. A. +PY - 2005 +TI - Conformational studies and solution structure of laulimalide and simplified analogues using NMR spectroscopy and molecular modelling +SP - 3677-3682 +N1 - MAY 23 2005 +JF - Tet. Lett. +VL - 46 +IS - (21) +N1 - Conformational studies and solution structure of laulimalide and simplified analogues using NMR spectroscopy and molecular modelling +N1 - Goodman +ID - 173 +ER - + +TY - JOUR +AU - Nerukh, D. +AU - Luzanov, A. V. +PY - 2005 +TI - Chirality measure of Leu-Enkephalin conformational transition during beta-turn formation +JF - Phys. Chem. Chem. Phys. +VL - submitted +N1 - Chirality measure of Leu-Enkephalin conformational transition during beta-turn formation +ID - 148 +ER - + +TY - JOUR +AU - Nerukh, D. +AU - Karvounis, G. +AU - Glen, R.C. +PY - 2005 +TI - Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding +JF - J. Chem. Phys. +VL - submitted +N1 - Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding +ID - 147 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Mitchell, J.B. +AU - Rzepa, H.S. +PY - 2005 +TI - Chemistry in Bioinformatics, +JF - BMC Bioinformatics +VL - 6 +IS - 141 +N1 - Chemistry in Bioinformatics, +ID - 153 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Mitchell, J.B.O. +AU - H.S. Rzepa +PY - 2005 +TI - Communication and re-use of chemical information in bioscience +SP - 180 +JF - BMC Bioinformatics +VL - 6 +N1 - Communication and re-use of chemical information in bioscience +N1 - Mitchell, +Murray Rust +UR - http://www.biomedcentral.com/1471-2105/6/180/abstract +ID - 165 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Stewart, J. J. P. +AU - Zhang, Y. +PY - 2005 +TI - A global resource for computational chemistry +JF - J. Mol. Mod. +N1 - A global resource for computational chemistry +N1 - Murray-Rust +ID - 182 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2005 +TI - XML, Chemical Markup Language (CML) and the Datument +JF - ACS Style Guide +VL - in press +N1 - XML, Chemical Markup Language (CML) and the Datument +N1 - Murray Rust +ID - 184 +ER - + +TY - JOUR +AU - Macleod, N.A. +AU - Butz, P. +AU - Simons, J. P. +AU - Grant, G H. +AU - Baker, C.M. +AU - Tranter, G E. +PY - 2005 +TI - Structure and electronic circular dichroism spectroscopy of chiral molecules in the gas phase and in solution: a computational and experimental investigation of neutral, hydrated and protonated 1-(R)-phenylethylamine and 1-(R)-phenylethanol +SP - 1432-1440 +JF - PCCP +VL - 7 +N1 - Structure and electronic circular dichroism spectroscopy of chiral molecules in the gas phase and in solution: a computational and experimental investigation of neutral, hydrated and protonated 1-(R)-phenylethylamine and 1-(R)-phenylethanol +N1 - Grant +ID - 170 +ER - + +TY - JOUR +AU - Luzanov, A V +AU - Nerukh, D +PY - 2005 +TI - Complexity and Chirality Indices for Molecular Informatics: Differential Geometry Approaches +SP - 55 +JF - Functional materials +VL - 12 +IS - 1 +N1 - Complexity and Chirality Indices for Molecular Informatics: Differential Geometry Approaches +N1 - Glen +ID - 146 +ER - + +TY - JOUR +AU - Kirtay, C. Konstantinou +AU - Mitchell, J. B. O. +AU - Lumley, J. A +PY - 2005 +TI - Knowledge Based Potentials: the Reverse Boltzmann Methodology, Virtual Screening and Molecular Weight Dependence +SP - 527-536 +JF - QSAR & Combinatorial Science +VL - 24 +N1 - Knowledge Based Potentials: the Reverse Boltzmann Methodology, Virtual Screening and Molecular Weight Dependence +N1 - Mitchell +ID - 154 +ER - + +TY - JOUR +AU - Kirby, A. J. +AU - Dutta-Roy, N. +AU - Silva, D. da +AU - Goodman, J. M. +AU - Lima, M. F. +AU - Roussev, C. D. +AU - Nome, F. +PY - 2005 +TI - Intramolecular General Acid Catalysis of Phosphate Transfer. Nucleophilic Attack by Oxyanions on the PO32- Group +SP - 7033-7040 +JF - J. Am. Chem. Soc. +VL - 127 +N1 - Intramolecular General Acid Catalysis of Phosphate Transfer. Nucleophilic Attack by Oxyanions on the PO32- Group +N1 - DOI: 10.1021/ja0502876 +N1 - Goodman +ID - 161 +ER - + +TY - JOUR +AU - Karthikeyan, M. +AU - Bender, A. +PY - 2005 +TI - Encoding and Decoding Molecular Structures as Two-Dimensional (PDF417) Barcodes +SP - 572 – 580 +JF - J. Chem. Inf. Model. +VL - 45 +N1 - Encoding and Decoding Molecular Structures as Two-Dimensional (PDF417) Barcodes +N1 - Glen +ID - 157 +ER - + +TY - JOUR +AU - Karthikeyan, M. +AU - Glen, R. C. +AU - Bender, A. +PY - 2005 +TI - Prediction of melting points of a diverse compound dataset using artificial neural networks +SP - 581 - 590 +JF - J. Chem. Inf. Model. +VL - 45 +N1 - Prediction of melting points of a diverse compound dataset using artificial neural networks +N1 - Glen +ID - 156 +ER - + +TY - JOUR +AU - Huggins, D. +AU - G.H. Grant +PY - 2005 +TI - A mechanism for activation, desensitization and inhibition of NMDA receptors +SP - 381-388 +JF - J. Mol. Graphics Modelling +VL - 23 +N1 - A mechanism for activation, desensitization and inhibition of NMDA receptors +N1 - Grant +ID - 168 +ER - + +TY - JOUR +AU - Huang, M. +AU - Grant, G.H. +AU - Richards, W.G. +PY - 2005 +TI - Diketo acid HIV-1 integrase inhibitors: an ab initio study +SP - 5198-5202 +JF - J. Phys. Chem. A, +VL - 109 +N1 - Diketo acid HIV-1 integrase inhibitors: an ab initio study +N1 - Grant +ID - 171 +ER - + +TY - JOUR +AU - Holliday, G L +AU - Bartlett, G J +AU - Almonacid, D E +AU - O’Boyle, N M +AU - Murray-Rust, P +AU - Thornton, J M +AU - Mitchell, J B O +PY - 2005 +TI - MACiE: A Database of Enzyme Reaction Mechanisms +SP - 4315-4316 +N1 - September 27, 2005 +JF - Bioinformatcs +VL - 21 +N1 - MACiE: A Database of Enzyme Reaction Mechanisms +N1 - doi:10.1093/bioinformatics/bti693 +N1 - Mitchell +Murray Rust +ID - 174 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 2005 +TI - Molecule Impossible +SP - 18-19 +N1 - 21 March 2005 +JF - Chemistry & Industry +VL - #6 +N1 - Molecule Impossible +N1 - Goodman +ID - 163 +ER - + +TY - JOUR +AU - Garcia, F. +AU - Goodman, J. M. +AU - Kowenicki, R. A. +AU - McPartlin, M. +AU - Riera, L. +AU - Silva, M. A. +AU - Wirsing, A. +AU - Wright, D. S. +PY - 2005 +TI - Selection of the cis and trans phosph(III)azane macrocycles [{P(_-NtBu)}2(1-Y-2-NH-C6H4)]2(Y = O, S) +SP - 1764-1773 +JF - Dalton Transactions +VL - 10 +N1 - Selection of the cis and trans phosph(III)azane macrocycles [{P(_-NtBu)}2(1-Y-2-NH-C6H4)]2(Y = O, S) +N1 - DOI: 10.1039/b502200b +N1 - Goodman +ID - 162 +ER - + +TY - JOUR +AU - Fergus, S. +AU - Bender, A. +AU - Spring, D. R. +PY - 2005 +TI - Assessment of Structural Diversity in Combinatorial Synthesis. +SP - 304 – 309 +JF - Curr. Opin. Chem. Biol. +VL - 9 +N1 - Assessment of Structural Diversity in Combinatorial Synthesis. +N1 - Glen +ID - 159 +ER - + +TY - JOUR +AU - Dubos, C. +AU - Willment, J. +AU - Huggins, D. +AU - Grant, G.H. +AU - Campbell, M.M. +PY - 2005 +TI - Kanamycin reveals the role played by glutamate receptors in shaping plant resource allocation +SP - 348-355 +JF - The Plant Journal +VL - 43 +N1 - Kanamycin reveals the role played by glutamate receptors in shaping plant resource allocation +N1 - Grant +ID - 172 +ER - + +TY - CONF +AU - Dove, M. T. +AU - White, T. O. +AU - Bruin, R.P. +AU - Tucker, M.G. +AU - Calleja, M. +AU - Artacho, E +AU - Murray-Rust, P +AU - Tyer, R P +AU - Todorov, I +AU - Allan, R J +AU - Dam, K Kleese van +AU - Smith, W +AU - Chapman, C +AU - Emmerich, W +AU - Marmier, A +AU - Parker, S C +AU - Lewis, G J +AU - Hasan, S M +AU - Thandavan, A +AU - Alexandrov, V +AU - Blanchard, M +AU - Wright, K +AU - Catlow, C R A +AU - Du, Z +AU - Leeuw, N H de +AU - Alfredsson, M +AU - Price, G D +AU - Brodholt, J +PY - 2005 +TI - eScience usability: the eMinerals experience +BT - Proceedings of the UK e-Science All Hands Meeting 2005 +VL - 425 +N1 - eScience usability: the eMinerals experience +N1 - Murray-Rust +ID - 186 +ER - + +TY - JOUR +AU - Diaz, J. +AU - Silva, M. A. +AU - Goodman, J. M. +AU - Pellegrinet, S. C. +PY - 2005 +TI - Computer-assisted design of asymmetric 1,3-dipolar cycloadditions between dimethylvinylborane and chiral nitrones +SP - 10886-10893 +JF - Tetrahedron +VL - 61 +N1 - Computer-assisted design of asymmetric 1,3-dipolar cycloadditions between dimethylvinylborane and chiral nitrones +N1 - DOI: 10.1016/j.tet.2005.09.004 +N1 - Goodman +ID - 175 +ER - + +TY - CONF +AU - Couch, P A +AU - Sherwood, P +AU - Sufi, S +AU - Todorov, I T +AU - Allan, R J +AU - Knowles, P J +AU - Bruin, R P +AU - Dove, M T +AU - Murray-Rust, P +PY - 2005 +TI - Towards Data Integration for Computational Chemistry +BT - Proceedings of the UK e-Science All Hands Meeting +VL - 509 +N1 - Towards Data Integration for Computational Chemistry +N1 - Murray-Rust +ID - 187 +ER - + +TY - JOUR +AU - Coles, S. J. +AU - Day, N. E. +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Zhang, Y. +PY - 2005 +TI - Enhancement of the Chemical Semantic Web through INChIfication +SP - 1832-1834 +JF - Org. Biomol. Chem. +VL - 3 +N1 - Enhancement of the Chemical Semantic Web through INChIfication +N1 - Murray-Rust +ID - 183 +ER - + +TY - JOUR +AU - Claridge, T.D.W. +AU - Long, D.D. +AU - Baker, C.M. +AU - Odell, B. +AU - Grant, G.H. +AU - Edwards, A.E. +AU - Tranter, G.E. +AU - Fleet, G.W.J. +AU - Smith, M.D. +PY - 2005 +TI - Helix-forming carbohydrate amino acids +JF - J. Org. Chem +VL - 70 +IS - 2082-2090 +N1 - Helix-forming carbohydrate amino acids +N1 - Grant +ID - 169 +ER - + +TY - JOUR +AU - Bender, A +AU - Glen, R. C. +PY - 2005 +TI - A Discussion of Measures of Enrichment in Virtual Screening: Comparing +the Information Content of Descriptors with Increasing Levels of +Sophistication +SP - 1369 – 1375 +JF - J. Chem. Inf. Model +VL - 45. +N1 - ASAP Article +N1 - A Discussion of Measures of Enrichment in Virtual Screening: Comparing +the Information Content of Descriptors with Increasing Levels of +Sophistication +N1 - Glen +ID - 166 +ER - + +TY - CHAP +AU - Bender, A +AU - Klamt, A +AU - Wichmann, K +AU - Thormann, M +AU - Glen, R C +PY - 2005 +BT - Lecture Notes in Bioinformatics +ED - Istrail, S. +ED - Pevzner, P. +ED - Waterman, M. +CT - Molecular Similarity Searching Using COSMO Screening Charges (COSMO/3PP) +PB - Springer. +CP - 3695 +A3 - editors), (Volume +ED - Berthold, Michael R. +ED - Glen, Robert C. +ED - Diedrichs, Kay +ED - Kohlbacher, Oliver +ED - Fischer, Ingrid +SP - 175 – 185 +N1 - Molecular Similarity Searching Using COSMO Screening Charges (COSMO/3PP) +SN - ISSN-0302-9743 +N1 - Glen +ID - 179 +ER - + +TY - JOUR +AU - Bender, A. +AU - Mussa, H. Y. +AU - Glen, R. C. +PY - 2005 +TI - Screening for DHFR inhibitors using MOLPRINT 2D, a fast fragment-based method employing the Naïve Bayesian Classifier: Limitations of the descriptor and the importance of balanced chemistry in training and test sets +SP - 658 - 666 +JF - J. Biomol. Screen +VL - 10 +N1 - Screening for DHFR inhibitors using MOLPRINT 2D, a fast fragment-based method employing the Naïve Bayesian Classifier: Limitations of the descriptor and the importance of balanced chemistry in training and test sets +N1 - Glen +ID - 155 +ER - + +TY - JOUR +AU - Townsend, J. A. +AU - Adams, S. E. +AU - Waudby, C. A. +AU - Souza, V. K. de +AU - Goodman, J. M. +AU - Murray-Rust, P. +PY - 2004 +TI - Chemical documents: machine understanding and automated information extraction +SP - 3294-3300 +JF - Org. Biomol. Chem +VL - 2 +N1 - Chemical documents: machine understanding and automated information extraction +N1 - Murray-Rust +ID - 26 +ER - + +TY - JOUR +AU - Takane, S. +AU - Mitchell, J.B.O. +PY - 2004 +TI - A structure-odour relationship study using EVA descriptors and hierarchical clustering +SP - 3250-3255 +JF - Organic & Biomolecular Chemistry +VL - 2 +N1 - A structure-odour relationship study using EVA descriptors and hierarchical clustering +N1 - Mitchell +ID - 112 +ER - + +TY - JOUR +AU - Socorro, I. +AU - Neels, A. +AU - Stoeckli-Evans, H. +PY - 2004 +TI - AgI and CuI binuclear macrocyclic complexes with 1-(3-pyridyl)ethanone oxime +SP - m13-m15 +JF - Acta Cryst. +VL - C60 +N1 - AgI and CuI binuclear macrocyclic complexes with 1-(3-pyridyl)ethanone oxime +N1 - Goodman +ID - 177 +ER - + +TY - JOUR +AU - Silva, M. A. +AU - Bellenie, B. R. +AU - Goodman, J. M. +PY - 2004 +TI - Theoretical Study on the Selectivity of Asymmetric Sulfur Ylide Epoxidation Reaction +SP - 2559-2562 +JF - Org. Lett. +VL - 6 +N1 - Theoretical Study on the Selectivity of Asymmetric Sulfur Ylide Epoxidation Reaction +N1 - Goodman +ID - 29 +ER - + +TY - JOUR +AU - Pellegrinet, S. C. +AU - Silva, M. A. +AU - Goodman, J. M. +PY - 2004 +TI - A promising enantioselective Diels-Alder dienophile by computer-assisted rational design: 2,5-diphenyl-1-vinyl-borolane +SP - 209-214. +JF - J. Comp.-Aided Mol. Design +VL - 18 +N1 - A promising enantioselective Diels-Alder dienophile by computer-assisted rational design: 2,5-diphenyl-1-vinyl-borolane +ID - 30 +ER - + +TY - JOUR +AU - Nerukh, D +AU - Karvounis, G +AU - Glen, R C +PY - 2004 +TI - Quantifying the complexity of chaos in multi-basin multidimensional dynamics of molecular systems +SP - 40 - 46 +JF - Complexity +VL - 10 +IS - 2 +N1 - Quantifying the complexity of chaos in multi-basin multidimensional dynamics of molecular systems +N1 - Glen +ID - 149 +ER - + +TY - JOUR +AU - Nerukh, D. +AU - Griffiths, T. R. +PY - 2004 +TI - Real and imaginary parts of the vibrational relaxation of acetonitrile in its electrolyte solutions: new results for the dynamics of solvent molecules +SP - 83 - 97 +JF - J. Molecular Liquids +VL - 109 +IS - 2 +N1 - Real and imaginary parts of the vibrational relaxation of acetonitrile in its electrolyte solutions: new results for the dynamics of solvent molecules +N1 - Glen +ID - 150 +ER - + +TY - JOUR +AU - Mussa, H.Y. +AU - Lary, D.J. +AU - Glen, R.C. +PY - 2004 +TI - Building Structure-Property Predictive Models Using Data Assimilation +SP - (Accepted) +JF - J. Chem. Inf. Comput. Sci. +N1 - Building Structure-Property Predictive Models Using Data Assimilation +ID - 136 +ER - + +TY - JOUR +AU - Mussa, H. Y. +AU - Lary, D. J. +AU - Siddans, R. +PY - 2004 +TI - Calculating Biases Using Data Assimilation and Artificial Intelligence +SP - (In press). +JF - Chemometric and Intelligent Laboratory Systems +N1 - Calculating Biases Using Data Assimilation and Artificial Intelligence +ID - 137 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Williamson, M. J. +AU - Willighagen, E. L. +PY - 2004 +TI - Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregator +SP - 462-469 +JF - J. Chem. Inf. Comput. Sci. +VL - 44 +N1 - Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregator +ID - 107 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Tyrrell, S. M. +AU - Zhang, Y. +AU - Wakelin, J. J. +PY - 2004 +TI - CML Tools and Information Flow in the Computation of Solid State Properties, +SP - pp. in press +JF - Molecular Simulations +N1 - CML Tools and Information Flow in the Computation of Solid State Properties, +ID - 106 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Tyrrell, S. M. +AU - Zhang, Y. +AU - Wakelin, J. J. +PY - 2004 +TI - A global resource for computational chemistry +JF - J. Molecular Modeling +VL - accepted +N1 - A global resource for computational chemistry +ID - 105 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2004 +TI - The Next Big Thing: From Hypermedia to Datuments, +SP - art 248 +JF - Journal of Digital Information +VL - 5 +N1 - The Next Big Thing: From Hypermedia to Datuments, +ID - 108 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Tyrrell, S. M. +AU - Zhang, Y. +PY - 2004 +TI - Representation and use of chemistry in the global electronic age +SP - 3192-3203 +JF - Organic & Biomolecular Chemistry +VL - 2 +N1 - Representation and use of chemistry in the global electronic age +ID - 104 +ER - + +TY - JOUR +AU - Moloney, G. P. +AU - Garavelas, A. +AU - Martin, G. R. +AU - Maxwell, M. +AU - Glen, R. C. +PY - 2004 +TI - Synthesis and serotonergic activitiy of variously substituted (3-amido) phenylpiperazine derivatives and benzothiophene-4-piperazine derivatives: novel antagonists for the vascular 5-HT 1B receptor +SP - 305-321 +JF - European J. of Medicinal Chemistry +VL - 39 +N1 - Synthesis and serotonergic activitiy of variously substituted (3-amido) phenylpiperazine derivatives and benzothiophene-4-piperazine derivatives: novel antagonists for the vascular 5-HT 1B receptor +N1 - Glen +ID - 35 +ER - + +TY - JOUR +AU - Marsden, P. M. +AU - Puvanendrampillai, D. +AU - Mitchell, J. B. O. +AU - Glen, R. C. +PY - 2004 +TI - Predicting protein-ligand binding affinities: a low scoring game? +SP - 3267-3273 +JF - J. Organic & Biomolecular Chemistry +VL - 2 +N1 - Predicting protein-ligand binding affinities: a low scoring game? +N1 - DOI: 10.1039/B409570G +ID - 5 +ER - + +TY - JOUR +AU - Macleod, N.A. +AU - Butz, P. +AU - Simons, J.P. +AU - Grant, G.H. +AU - Baker, C.M. +PY - 2004 +TI - Electronic Circular Dichroism Spectroscopy of 1-(R)-Phenylethanol: the 'Sector Rule' Revisited and an Exploration of Solvent Effects +SP - 27-36 +JF - Isr. J. Chem +VL - 44 +N1 - Electronic Circular Dichroism Spectroscopy of 1-(R)-Phenylethanol: the 'Sector Rule' Revisited and an Exploration of Solvent Effects +N1 - Grant +ID - 167 +ER - + +TY - JOUR +AU - Macleod, N. A. +AU - Butz, P. +AU - Simons, J. P. +AU - Grant, G. H. +AU - Baker, C. M. +AU - Tranter, G. E. +PY - 2004 +TI - Structure and electronic circular dichroism spectroscopy of chiral molecules in the gas phase and in solution: a computational and experimental investigation of neutral, hydrated and protonated 1-(R)-phenylethanol +SP - 1432-1440 +JF - Phys. Chem. Chem. Phys. +VL - 7 +N1 - Structure and electronic circular dichroism spectroscopy of chiral molecules in the gas phase and in solution: a computational and experimental investigation of neutral, hydrated and protonated 1-(R)-phenylethanol +N1 - Grant +ID - 191 +ER - + +TY - JOUR +AU - Lary, D.J. +AU - Mussa, H.Y. +PY - 2004 +TI - Using an extended Kalman filter learning algorithm for feed-forward neural networks to describe tracer correlations +SP - 3653 +JF - Atmospheric Chemistry and Physics +IS - [4] +N1 - Using an extended Kalman filter learning algorithm for feed-forward neural networks to describe tracer correlations +N1 - Lary +ID - 139 +ER - + +TY - JOUR +AU - Lary, D.J. +AU - Muller, M. +AU - Mussa, H.Y. +PY - 2004 +TI - Using neural networks to describe tracer correlations +SP - 143 +JF - Atmospheric Chemistry and Physics +VL - 4 +N1 - Using neural networks to describe tracer correlations +ID - 138 +ER - + +TY - JOUR +AU - Karvounis, G. +AU - Nerukh, D. +AU - Glen, R. C. +PY - 2004 +TI - Water Network dynamics at the critical moment of the peptide's beta turn formation: A Molecular dynamics study +SP - 4925 - 4935 +JF - J. Chemical Physics +VL - 121 +IS - 10 +N1 - Water Network dynamics at the critical moment of the peptide's beta turn formation: A Molecular dynamics study +N1 - Glen +N1 - (reproduced in Virtual Journal of Biological Physics Research, 8 (2004)) +ID - 4 +ER - + +TY - JOUR +AU - Horsley, H. T. +AU - Holmes, A. B. +AU - Davies, J. E. +AU - Goodman, J. M. +AU - Silva, M. A. +AU - Pascu, S. I. +AU - Collins, I. +PY - 2004 +TI - Investigation of conjugate addition/intramolecular nitrone dipolar cycloadditions and their use in the synthesis of dendrobatid alkaloid precursors +SP - 1258-1265 +JF - Org. Biomol. Chem. +VL - 2 +N1 - Investigation of conjugate addition/intramolecular nitrone dipolar cycloadditions and their use in the synthesis of dendrobatid alkaloid precursors +ID - 32 +ER - + +TY - JOUR +AU - Holliday, G. L. +AU - Mitchell, J. B. O. +AU - Murray-Rust, P. +PY - 2004 +TI - CMLSnap: Animated Reaction Mechanisms, +JF - Internet Journal of Chemistry +VL - 7 +IS - 4 +N1 - CMLSnap: Animated Reaction Mechanisms, +ID - 33 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 2004 +TI - Chemistry on the world-wide-web: a ten year experiment +SP - 3222-3225 +JF - Org. Biomol. Chem. +VL - 2 +N1 - Chemistry on the world-wide-web: a ten year experiment +ID - 27 +ER - + +TY - JOUR +AU - Glen, R. C. +PY - 2004 +TI - Editorial on ŒNew Horizons in Molecular Informatics +JF - J Organic and Biomolecular Chemistry +VL - 1 +N1 - Editorial on ŒNew Horizons in Molecular Informatics +ID - 6 +ER - + +TY - JOUR +AU - Glen, R. C. +AU - Bender, A. +PY - 2004 +TI - Molecular similarity: a key technique in molecular informatics. Organic +and Biomolecular Chemistry perspective article. +SP - 3204 - 3218. +JF - Org. Biomol. Chem +IS - 2 +N1 - Molecular similarity: a key technique in molecular informatics. Organic +and Biomolecular Chemistry perspective article. +N1 - Glen +ID - 8 +ER - + +TY - JOUR +AU - Glen, R. C. +PY - 2004 +TI - New horizons in molecular informatics +SP - E5 +JF - RSC Organic & Biomolecular Chemistry +VL - 2 +N1 - New horizons in molecular informatics +ID - 103 +ER - + +TY - JOUR +AU - Garcia, F. +AU - Goodman, J. M. +AU - Kowenicki, R. A. +AU - Kuzu, I. +AU - McPartlin, M. +AU - Silva, M. A. +AU - Riera, L. +AU - Woods, A. D. +AU - Wright, D. S. +PY - 2004 +TI - Selection of a Pentameric Host in the Host–Guest Complexes {[{[P(m-NtBu)]2(m-NH)}5]·I}–[Li(thf)4]+ and [{[P(m-NtBu)]2(m-NH)}5]·HBr·THF +SP - 6066-6072 +JF - Chemistry - A European Journal +VL - 10 +N1 - Selection of a Pentameric Host in the Host–Guest Complexes {[{[P(m-NtBu)]2(m-NH)}5]·I}–[Li(thf)4]+ and [{[P(m-NtBu)]2(m-NH)}5]·HBr·THF +N1 - Goodman +ID - 25 +ER - + +TY - JOUR +AU - Bender, A. +AU - Mussa, H. Y. +AU - Glen, R. C. +AU - Reiling, S. +PY - 2004 +TI - Molecular Similarity Searching using Atom Environments, +Information-Based Feature Selection and a Naïve Bayesian Classifier. +SP - 170-178 +JF - J. Chem. Inf.Comput. Sci. +VL - 44 +IS - 1 +N1 - Molecular Similarity Searching using Atom Environments, +Information-Based Feature Selection and a Naïve Bayesian Classifier. +ID - 11 +ER - + +TY - JOUR +AU - Bender, A. +AU - Glen, R. C. +PY - 2004 +TI - Molecular similarity: a key technique in molecular informatics +SP - 3204-3218 +JF - Organic & Biomolecular Chemistry +VL - 2 +N1 - Molecular similarity: a key technique in molecular informatics +ID - 109 +ER - + +TY - JOUR +AU - Bender, A. +AU - Mussa, H. Y. +AU - Gill, G. S. +AU - Glen, R. C. +PY - 2004 +TI - Molecular surface point environments for virtual screening and the +elucidation of binding patterns (MOLPRINT 3D), +SP - 1021 +N1 - accepted. September 2004. +JF - J. Med. Chem +VL - 10 +N1 - Molecular surface point environments for virtual screening and the +elucidation of binding patterns (MOLPRINT 3D), +ID - 7 +ER - + +TY - JOUR +AU - Bender, A. +AU - Mussa, H. Y. +AU - Gill, G. S. +AU - Glen, R. C. +PY - 2004 +TI - Molecular surface point environments for virtual screening and the +elucidation of binding patterns (MOLPRINT) +SP - 6569 - 6583 +JF - J. Med. Chem. +VL - 47 +N1 - Molecular surface point environments for virtual screening and the +elucidation of binding patterns (MOLPRINT) +ID - 141 +ER - + +TY - JOUR +AU - Bender, A. +AU - Mussa, H. Y. +AU - Glen, R. C. +AU - Reiling, S. J. +PY - 2004 +TI - Similarity Searching of Chemical Databases Using Atom Environment +Descriptors (MOLPRINT 2D): Evaluation of Performance. +SP - 1708-1718 +JF - J. Chem. Inf. Comput. Sci. +VL - 44 +IS - 5 +N1 - Similarity Searching of Chemical Databases Using Atom Environment +Descriptors (MOLPRINT 2D): Evaluation of Performance. +ID - 9 +ER - + +TY - JOUR +AU - Bellenie, B. R. +AU - Goodman, J. M. +PY - 2004 +TI - Sulfonium ylide epoxidation reactions: methylene transfer +SP - 1076-1077 +JF - Chem. Comm. +N1 - Sulfonium ylide epoxidation reactions: methylene transfer +ID - 31 +ER - + +TY - JOUR +AU - Albrecht, B +AU - G.H., Grant +AU - Richards, W.G. +PY - 2004 +TI - Evaluation of structural similarity based on reduced dimensionality representations of protein structure +SP - 425–432 +JF - Protein Engineering, Design and Selection +VL - 17 +N1 - Evaluation of structural similarity based on reduced dimensionality representations of protein structure +N1 - Grant +ID - 190 +ER - + +TY - JOUR +AU - Adams, S. E. +AU - Goodman, J. M. +AU - Kidd, R. J. +AU - McNaught, A. D. +AU - Murray-Rust, P. +AU - Norton, F. R. +AU - Townsend, J. A. +AU - Waudby, C. A. +PY - 2004 +TI - Experimental data checker: better information for organic chemists +SP - 3067-3070 +JF - Org. Biomol. Chem. +VL - 2 +N1 - Experimental data checker: better information for organic chemists +N1 - Goodman +Murray Rust +N1 - • Highlighted in Chemical Science 2004, 1, C33 +ID - 28 +ER - + +TY - JOUR +AU - Xing, L. +AU - Glen, R. C. +AU - Clark, R. D. +PY - 2003 +TI - Predicting pKa by Molecular Tree Structured Fingerprints and PLS. +SP - 870-879 +JF - J. Chem. Inf. Comput. Sci. +VL - 43 +IS - (3) +N1 - Predicting pKa by Molecular Tree Structured Fingerprints and PLS. +ID - 22 +ER - + +TY - JOUR +AU - Walsh, L. M. +AU - Goodman, J. M. +PY - 2003 +TI - Stereochemical elucidation of the 1,4 polyketide amphidinoketide I +SP - 2616-2617 +JF - Chem. Comm. +N1 - Stereochemical elucidation of the 1,4 polyketide amphidinoketide I +ID - 116 +ER - + +TY - JOUR +AU - Stewart, C. R. +AU - Goodman, J. M. +PY - 2003 +TI - Rotavap Simulation and the Estimation of Boiling Points +SP - 2654-2655. +JF - Chem. Comm. +N1 - Rotavap Simulation and the Estimation of Boiling Points +N1 - Highlighted in: Reactive Reports December 2003, Issue 35. +ID - 117 +ER - + +TY - JOUR +AU - Silva, M.A. +AU - Pellegrine, S.C. +AU - Goodman, J. M. +PY - 2003 +TI - A DFT study on the regioselectivity of the reaction of dichloropropynylborane with isoprene +SP - 4059-4066 +N1 - 16.05.2003 +JF - J. Organic Chemistry +VL - 68 +IS - 10 +N1 - A DFT study on the regioselectivity of the reaction of dichloropropynylborane with isoprene +AD - Goodman JM, Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, +England +Univ Cambridge, Dept Chem, Cambridge CB2 1EW, England +Univ Nacl Rosario, Fac Ciencias Bioquim & Farmaceut, Inst Quim Organ +Sintesis, CONICET, RA-2000 Rosario, Santa Fe, Argentina +ID - 2 +ER - + +TY - JOUR +AU - Silva, M. A. +AU - Pellegrinet, S. C. +AU - Goodman, J. M. +PY - 2003 +TI - Diels-Alder Reactions of Vinylboranes: A Computational Study on the Boron Substituent Effects +SP - 556-565 +JF - ARKIVOC +VL - X +N1 - Diels-Alder Reactions of Vinylboranes: A Computational Study on the Boron Substituent Effects +ID - 45 +ER - + +TY - JOUR +AU - Silva, M. A. +AU - Goodman, J. M. +PY - 2003 +TI - QRC: A rapid method for connecting transition structures to reactants in the computational analysis of organic reactivity +SP - 8233-8236. +JF - Tet. Lett. +VL - 44 +N1 - QRC: A rapid method for connecting transition structures to reactants in the computational analysis of organic reactivity +ID - 118 +ER - + +TY - JOUR +AU - Ruzhitskaya, N. N. +AU - Nerukh, A. G. +AU - Nerukh, D. +PY - 2003 +TI - Accurate modelling of pulse transformation by adjustable-in-time medium parameters, +SP - 347-364 +JF - Optical and Quantum Electronics +VL - 35 +IS - (4) +N1 - Accurate modelling of pulse transformation by adjustable-in-time medium parameters, +ID - 151 +ER - + +TY - JOUR +AU - Puvanendrampillai, D. +AU - Mitchell, J.B.O. +PY - 2003 +TI - Protein Ligand Database (PLD): Additional Understanding of the Nature +and Specificity of Protein-Ligand Complexes +SP - 1856-1857 +JF - Bioinformatics +VL - 19 +N1 - Protein Ligand Database (PLD): Additional Understanding of the Nature +and Specificity of Protein-Ligand Complexes +ID - 1 +ER - + +TY - JOUR +AU - Ouvrard, C. +AU - Mitchell, J.B.O. +PY - 2003 +TI - Can we Predict Lattice Energy from Molecular Structure? +SP - 676-685 +JF - Acta Crystallographica +VL - B59 +N1 - Can we Predict Lattice Energy from Molecular Structure? +N1 - Mitchell +ID - 115 +ER - + +TY - JOUR +AU - Mussa, H. Y. +AU - Tennyson, J. +PY - 2003 +TI - Rovibrational Quasi-Bound States of HOCL +SP - 449 +JF - Chem. Phys. Lett. +VL - 366 +N1 - Rovibrational Quasi-Bound States of HOCL +ID - 133 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2003 +TI - Chemical Markup, XML, and the World Wide Web. 4. CML Schema +SP - 757-772 +JF - J. Chem. Inf. Comput. Sci. +VL - 43 +N1 - Chemical Markup, XML, and the World Wide Web. 4. CML Schema +ID - 124 +ER - + +TY - CHAP +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2003 +BT - Handbook of Chemoinformatics Volume 1 +ED - Engel, J. Gasteiger and T. +CT - Part 2. Advanced Topics. +N1 - Part 2. Advanced Topics. +N1 - Murray-Rust +ID - 50 +ER - + +TY - CONF +AU - Murray-Rust, P. +AU - Glen, R.C. +AU - Rzepa, H.S. +AU - Stewart, J.J.P. +AU - Townsend, J.A. +AU - Willighagen, E.L. +AU - Zhang, Y. +PY - 2003 +TI - A semantic GRID for molecular science +BT - Proceedings of UK e-Science All Hands Meeting +SP - 802-809 +N1 - A semantic GRID for molecular science +ID - 122 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2003 +TI - Towards the Chemical Semantic Web. An introduction to RSS +SP - pp. art 4 +JF - J. Chem. +VL - 6 +N1 - Towards the Chemical Semantic Web. An introduction to RSS +ID - 120 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2003 +TI - XML for scientific publishing +SP - 162-169 +JF - OCLC Systems and Services +VL - 19 +N1 - XML for scientific publishing +ID - 123 +ER - + +TY - JOUR +AU - Mitchell, J.B.O. +AU - Smith, J. +PY - 2003 +TI - D-Amino Acid Residues in Peptides and Proteins +SP - 563-571 +JF - Proteins: Structure, Function and Genetics +IS - 50 +N1 - D-Amino Acid Residues in Peptides and Proteins +ID - 125 +ER - + +TY - JOUR +AU - Lary, D. J. +AU - Khattatov, B. +AU - Mussa, H. Y. +PY - 2003 +TI - Chemical Data Assimilation: A Case Study of Solar Occultation Data From the Atlas 1 Mission of the Atmospheric Trace Molecule Spectroscopy Experiment +SP - 4456 +JF - J. Geophys. Res. +VL - 108 +IS - (D15) +N1 - Chemical Data Assimilation: A Case Study of Solar Occultation Data From the Atlas 1 Mission of the Atmospheric Trace Molecule Spectroscopy Experiment +N1 - doi:10.1029/2003JD003500, 2003. +ID - 135 +ER - + +TY - JOUR +AU - Kostin, M. A. +AU - Mussa, H. Y. +AU - Polyansky, O. L. +AU - Tennyson, J. +PY - 2003 +TI - Calculation of Rovibrational States of H_{3}^{+} up to Dissociation +SP - 3538 +JF - J. of Chem. Phys. +VL - 118 +N1 - Calculation of Rovibrational States of H_{3}^{+} up to Dissociation +ID - 134 +ER - + +TY - JOUR +AU - Holliday, G.L. +AU - Bartlett, G.J. +AU - Murray-Rust, P. +AU - Thornton, J.M. +AU - Mitchell, J.B.O. +PY - 2003 +TI - Classification and Computer Representation of Enzyme Reactions. Progress Towards the Development of MACiE +SP - 099-CINF Part 1 +N1 - SEP 2003 +JF - Abstracts of Papers of the American Chemical Society +VL - 226 +N1 - Classification and Computer Representation of Enzyme Reactions. Progress Towards the Development of MACiE +ID - 113 +ER - + +TY - JOUR +AU - Haustedt, L. O. +AU - Goodman, J. M. +PY - 2003 +TI - How Accurate Is the Steady State Approximation? +SP - 839 +JF - J. Chem. Educ. +VL - 80 +N1 - How Accurate Is the Steady State Approximation? +ID - 119 +ER - + +TY - MGZN +AU - Goodman, J. M. +PY - 2003 +TI - Desktop Molecular Modeller +BT - Physical Sciences Educational Reviews +VL - 4 +IS - 2 +SP - 33-34 +N1 - Desktop Molecular Modeller +ID - 47 +ER - + +TY - MGZN +AU - Goodman, J. M. +PY - 2003 +TI - Drug design: cutting edge approaches +BT - Chemistry & Industry +IS - 16 +SP - 23-24 +N1 - 18th August 2003 +N1 - Drug design: cutting edge approaches +ID - 46 +ER - + +TY - CONF +AU - Goodman, J. M. +AU - Bellenie, B. R. +PY - 2003 +TI - Highly enantioselective sulfur ylide epoxidation reactions +BT - 225th ACS National Meeting +CY - New Orleans. March 23-27 +VL - ORGN 446 +N1 - Highly enantioselective sulfur ylide epoxidation reactions +ID - 48 +ER - + +TY - CONF +AU - Goodman, J. M. +AU - Makiyi, E. F. +AU - Donald, A. D. G. +PY - 2003 +TI - Studies towards the total synthesis of dolabriferol +BT - 225th ACS National Meeting, +CY - New Orleans. March 23-27 +VL - ORGN 416 +N1 - Studies towards the total synthesis of dolabriferol +ID - 49 +ER - + +TY - JOUR +AU - Glen, R. C. +AU - Allen, S. C. +PY - 2003 +TI - Ligand-protein docking: cancer research at the interface between biology and chemistry +SP - 767-782 +JF - Current Medicinal Chemistry +VL - 10 +IS - 9 +N1 - Ligand-protein docking: cancer research at the interface between biology and chemistry +ID - 12 +ER - + +TY - JOUR +AU - Gkoutos, G. V. +AU - Rzepa, H. S. +AU - Murray-Rust, P. +PY - 2003 +TI - Online Validation and Comparison of Molfile and CML Molecular Atom-Connection Descriptor +SP - article 1 +JF - Internet J. Chem +VL - 6 +N1 - Online Validation and Comparison of Molfile and CML Molecular Atom-Connection Descriptor +ID - 51 +ER - + +TY - JOUR +AU - Gibson, M. +AU - Goodman, J. M. +AU - Farrugia, L. J. +AU - Hartley, R. C. +PY - 2003 +TI - Controlling neighbouring group participation from thioacetals +SP - 2841-2844 +JF - Tetrahedron Letters 2003 +VL - 44 +N1 - Controlling neighbouring group participation from thioacetals +ID - 39 +ER - + +TY - CONF +AU - Dove, M. T +AU - Calleja, M. +AU - Wakelin, J. +AU - Trachenko, K. +AU - Ferlat, G. +AU - Murray-Rust, P. +AU - Leeuw, N. H. de +AU - Du, Z. +AU - Price, G. D. +AU - Wilson, P. B +AU - Brodholt, J. P. +AU - Alfredsson, M. +AU - Marmier, A. +AU - Tyer, R. P. +AU - Blanshard, L. J. +AU - Allan, R. J. +AU - Dam, K. Kleese van +AU - Todorov, I. T. +AU - Smith, W. +AU - Alexandrov, V. N. +AU - Lewis, G. J. +AU - Thandavan, A. +AU - Hasan, S. Mehmood +PY - 2003 +TI - Environment from the molecular level: an escience testbed project +BT - Proceedings of UK e-Science All Hands Meeting +SP - 302-309 +N1 - Environment from the molecular level: an escience testbed project +ID - 121 +ER - + +TY - JOUR +AU - Davies, J. E. +AU - Fleming, I. +AU - Goodman, J. M. +PY - 2003 +TI - A tricycloheptane product in cationic rearrangements +SP - 3570-3571 +JF - Organic and Biomolecular Chemistry +VL - 1 +N1 - A tricycloheptane product in cationic rearrangements +ID - 41 +ER - + +TY - JOUR +AU - Bailey, J. +AU - Kettle, L.J. +AU - Cherryman, J.C. +AU - Mitchell, J.B.O. +PY - 2003 +TI - Triazinone Tautomers: Solid Phase Energetics +SP - 498-502 +JF - CrystEngComm +VL - 5 +N1 - Triazinone Tautomers: Solid Phase Energetics +ID - 114 +ER - + +TY - JOUR +AU - Winn, C. L. +AU - Bellenie, B. R. +AU - Goodman, J. M. +PY - 2002 +TI - A highly enantioselective one-pot sulfur ylide epoxidation reaction +SP - 5427-5430 +JF - Tetrahedron Letters +VL - 43 +N1 - A highly enantioselective one-pot sulfur ylide epoxidation reaction +ID - 128 +ER - + +TY - JOUR +AU - Walsh, L. M. +AU - L.Winn, C. +AU - Goodman, J. M. +PY - 2002 +TI - Sulfide-BF3.OEt2 mediated Baylis-Hillman reactions +SP - 8219-8222 +JF - Tetrahedron Letters +VL - 43 +N1 - Sulfide-BF3.OEt2 mediated Baylis-Hillman reactions +ID - 126 +ER - + +TY - JOUR +AU - Silva, M. A. +AU - Goodman, J. M. +PY - 2002 +TI - Nitrone cyclisations: the development of a semi-quantitative model from ab initio calculations +SP - 3667-3671 +JF - Tetrahedron Letters +VL - 58 +N1 - Nitrone cyclisations: the development of a semi-quantitative model from ab initio calculations +ID - 55 +ER - + +TY - JOUR +AU - Silva, M. A. +AU - Pellegrinet, S. C. +AU - Goodman, J. M. +PY - 2002 +TI - A theoretical study of the reaction of alkynylboranes with butadiene: competition between cycloaddition and alkynylboration +SP - 8203-8209 +JF - J. Org. Chem. +VL - 67 +N1 - A theoretical study of the reaction of alkynylboranes with butadiene: competition between cycloaddition and alkynylboration +ID - 54 +ER - + +TY - JOUR +AU - Nerukh, D. +AU - Karvounis, G. +AU - Glen, R. C. +PY - 2002 +TI - Complexity of classical dynamics of molecular systems Part 1. methodology. +SP - 9611-9617 +JF - J. Chem. Phys. +VL - 117 +N1 - Complexity of classical dynamics of molecular systems Part 1. methodology. +ID - 19 +ER - + +TY - JOUR +AU - Nerukh, D. +AU - Karvounis, G. +AU - Glen, R. C. +PY - 2002 +TI - Complexity of classical dynamics of molecular systems Part 2. Finite statistical complexity of a water-Na+ system +SP - 9618-9622 +JF - J. Chem. Phys. +VL - 117 +N1 - Complexity of classical dynamics of molecular systems Part 2. Finite statistical complexity of a water-Na+ system +ID - 20 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2002 +TI - Markup Languages - How to structure chemistry-related documents +JF - Chemistry International +VL - 24 +N1 - Markup Languages - How to structure chemistry-related documents +ID - 60 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H.S. +PY - 2002 +TI - Markup Languages - How to Structure Chemistry-Related Documents +JF - Chemistry International +VL - 24 +N1 - Markup Languages - How to Structure Chemistry-Related Documents +ID - 131 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2002 +TI - Scientific publications in XML - towards a global knowledge base +SP - 84-98 +JF - Data Science +VL - 1 +N1 - Scientific publications in XML - towards a global knowledge base +ID - 58 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2002 +TI - STMML. A markup language for scientific, technical and medical publishing. +SP - 1-65 +JF - Data Science +VL - 1 +N1 - STMML. A markup language for scientific, technical and medical publishing. +ID - 59 +ER - + +TY - CHAP +AU - Murray-Rust, P. +AU - Glen, R. C. +AU - Zhang, Y. +AU - Harter, J. +PY - 2002 +BT - EuroWeb2002, The Web and the GRID: from e-science to e-business +ED - Matthews, B. +ED - Hopgood, B. +ED - M.Wilson +CT - The World Wide Molecular Matrix - a peer-to-peer XML repository for +molecules and properties +PB - The British Computer Society. +SP - 163-164 +N1 - The World Wide Molecular Matrix - a peer-to-peer XML repository for +molecules and properties +ID - 21 +ER - + +TY - MGZN +AU - Mitchell, J. B. O. +PY - 2002 +TI - Review of ‘Computational Chemistry by D Young’ +BT - Chemistry & Industry +SP - 23-24 +N1 - 15.07.02 +N1 - Review +N1 - Review of ‘Computational Chemistry by D Young’ +ID - 56 +ER - + +TY - MGZN +AU - Mitchell, J. B. O. +PY - 2002 +TI - Review of ‘Introduction to Bioinformatics’ (A Lesk) +BT - Natural Product Reports +VL - 19 +SP - 782 +N1 - Review of ‘Introduction to Bioinformatics’ (A Lesk) +N1 - Editor A. Lesk, +ID - 57 +ER - + +TY - CONF +AU - Harter, J. +AU - Zhang, Y. +AU - Murray-Rust, P. +AU - Glen, R. C. +PY - 2002 +TI - World Wide Molecular Matrix +BT - EuroWeb Conference +CY - Oxford +N1 - World Wide Molecular Matrix +ID - 53 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 2002 +TI - Curly Arrows: Writing Organic Reaction Mechanisms +JF - Physical Sciences Educational Reviews +VL - 3 +IS - 1 +N1 - Curly Arrows: Writing Organic Reaction Mechanisms +ID - 142 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 2002 +TI - How well are we using XML in Chemistry? +SP - 7 +JF - Chemistry International +VL - 24 +N1 - How well are we using XML in Chemistry? +ID - 127 +ER - + +TY - JOUR +AU - Glen, R. C. +AU - Aldridge, S. +PY - 2002 +TI - Developing tools and standards in molecular informatics. +SP - 2745-2747. +JF - Chem. Comm. +N1 - Focus +N1 - Developing tools and standards in molecular informatics. +ID - 23 +ER - + +TY - JOUR +AU - Glen, R. C. +AU - Xing, L. +PY - 2002 +TI - Novel methods for the prediction of pKa, logP and logD +SP - 796-805 +JF - J. Chem. Inf. Comput. Sci. +VL - 42 +IS - (4) +N1 - Novel methods for the prediction of pKa, logP and logD +ID - 18 +ER - + +TY - JOUR +AU - Chugh, J. K. +AU - Brückner, H. +AU - Wallace, B. A. +PY - 2002 +TI - Model for a Helical Bundle Channel Based on the High resolution crystal structure of Trihotoxin_A50E +SP - 12934-12941 +JF - Biochemistry +VL - 41 +N1 - Model for a Helical Bundle Channel Based on the High resolution crystal structure of Trihotoxin_A50E +ID - 37 +ER - + +TY - JOUR +AU - Winn, C. L. +AU - Goodman, J. M. +PY - 2001 +TI - Studies on the formation of a tricyclic C2-symmetric sulfide +SP - 7091-7093 +JF - Tet. Lett. +VL - 42 +N1 - Studies on the formation of a tricyclic C2-symmetric sulfide +ID - 65 +ER - + +TY - JOUR +AU - Wallace, D. J. +AU - Goodman, J. M. +AU - Kennedy, D. J. +AU - Davies, A. J. +AU - Cowden, C. J. +AU - Ashwood, M. S. +AU - Cottrell, I. F. +AU - Dolling, U. H. +AU - Reider, P. J. +PY - 2001 +TI - A double ring closing metathesis reaction in the rapid, enantioselective synthesis of NK-1 receptor antagonists +SP - 671-674 +JF - Org. Lett. +VL - 3 +N1 - A double ring closing metathesis reaction in the rapid, enantioselective synthesis of NK-1 receptor antagonists +ID - 72 +ER - + +TY - JOUR +AU - Torres, J. +AU - Kukol, A. +AU - Goodman, J. M. +AU - Arkin, I. T. +PY - 2001 +TI - Site-specific examination of secondary structure and orientation determination in membrane proteins: the peptidic 13C=18O group as a novel infrared probe +SP - 396-401 +JF - Biopolymers +VL - 59 +N1 - Site-specific examination of secondary structure and orientation determination in membrane proteins: the peptidic 13C=18O group as a novel infrared probe +ID - 62 +ER - + +TY - JOUR +AU - Smith, E.D.L. +AU - Hammond, R.B. +AU - Roberts, K.J. +AU - Jones, M.J. +AU - Mitchell, J.B.O. +AU - Price, S.L. +AU - Harris, R.K. +AU - Apperley, D.C. +AU - Cherryman, J.C. +AU - Docherty, R. +PY - 2001 +TI - The Determination of the Crystal Structure of Anhydrous Theophylline by X-ray Powder Diffraction with a Systematic Search Algorithm, Lattice Energy Calculations and 13C and 15N Solid-state NMR: A Question of Polymorphism in a Given Unit Cell +SP - 5818-5826 +JF - J. Phys. Chem. B +VL - 105 +N1 - The Determination of the Crystal Structure of Anhydrous Theophylline by X-ray Powder Diffraction with a Systematic Search Algorithm, Lattice Energy Calculations and 13C and 15N Solid-state NMR: A Question of Polymorphism in a Given Unit Cell +ID - 61 +ER - + +TY - JOUR +AU - Selwood, D. L. +AU - Brummell, D.G. +AU - Glen, R. C. +AU - Goggin, M.C. +AU - Reynolds, K. +AU - Tatlock, M. A. +AU - Wishart, G. +PY - 2001 +TI - Solution-Phase parallel synthesis of 5-carboxamido 1-benzyl 3(3dimethylaminopropyloxy)1H-pyrazoles as activators of soluble +guanylate cyclase with improved oral bioavailability +SP - 1089-1092 +N1 - 23 April 2001 +JF - Bioorg. Med. Chem. Lett. +VL - 11 +IS - (8) +N1 - Solution-Phase parallel synthesis of 5-carboxamido 1-benzyl 3(3dimethylaminopropyloxy)1H-pyrazoles as activators of soluble +guanylate cyclase with improved oral bioavailability +ID - 17 +ER - + +TY - JOUR +AU - Selwood, D. L. +AU - Brummell, D. G. +AU - Budworth, J. +AU - Burtin, G. E. +AU - Campbell, R.O. +AU - Chana, S. S. +AU - Charles, I. G. +AU - Fernandez, P. A. +AU - Glen, R. C. +AU - Goggin, M. C. +AU - Hobbs, A. J. +AU - Kling, M. R. +AU - Liu, Q. +AU - Madge, D. J. +AU - Meillerais, S. +AU - Powell, K. L. +AU - Reynolds, K. +AU - Spacey, G. D. +AU - Stables, J. N. +AU - Tatlock, M. A. +AU - Wheeler, K. A. +AU - Wishart, G. +AU - Woo, C-K +PY - 2001 +TI - Synthesis and Biological Evaluation of Novel Pyrazoles and Indazoles as +Activators of the Nitric Oxide Receptor, Soluble Guanylate Cyclase. +SP - 78-93 +JF - J. Med. Chem +VL - 44 +IS - (1) +N1 - Synthesis and Biological Evaluation of Novel Pyrazoles and Indazoles as +Activators of the Nitric Oxide Receptor, Soluble Guanylate Cyclase. +ID - 13 +ER - + +TY - JOUR +AU - Rzepa, H. S. +AU - Murray-Rust, P. +PY - 2001 +TI - A new publishing paradigm: STM articles as part of the semantic web. +SP - 177 +JF - Learned Publishing +VL - 14 +N1 - A new publishing paradigm: STM articles as part of the semantic web. +ID - 81 +ER - + +TY - JOUR +AU - Rutherford, A. P. +AU - Gibb, C. S. +AU - Hartley, R. C. +AU - Goodman, J. M. +PY - 2001 +TI - Stereocontrol in a one-pot procedure for anionic oxy-Cope rearrangement followed by intramolecular aldol reaction +SP - 1051-1061 +JF - J. Chem. Soc. +VL - 1 +IS - Perkin Trans. +N1 - Stereocontrol in a one-pot procedure for anionic oxy-Cope rearrangement followed by intramolecular aldol reaction +ID - 69 +ER - + +TY - JOUR +AU - Pellegrinet, S. C. +AU - Silva, M. A. +AU - Goodman, J. M. +PY - 2001 +TI - Theoretical evaluation of the origin of the regio- and stereoselectivity in the Diels-Alder reactions of dialkylvinylboranes: Studies on the reactions of vinylborane, dimethylvinylborane, and vinyl-9-BBN with trans-piperylene and isoprene +SP - 8832-8837 +JF - J. Am. Chem. Soc. +VL - 123 +N1 - Theoretical evaluation of the origin of the regio- and stereoselectivity in the Diels-Alder reactions of dialkylvinylboranes: Studies on the reactions of vinylborane, dimethylvinylborane, and vinyl-9-BBN with trans-piperylene and isoprene +ID - 67 +ER - + +TY - JOUR +AU - Nobeli, I. +AU - Mitchell, J. B. O. +AU - Alex, A. +AU - Thornton, J. M. +PY - 2001 +TI - Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes +SP - 673-688 +JF - J. Comp. Chem. +VL - 22 +N1 - Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes +ID - 75 +ER - + +TY - JOUR +AU - Nerukh, D. +AU - Griffiths, T. R. +PY - 2001 +TI - Complex vibrational correlation functions extracted from the resolved 2 band of liquid acetonitrile +SP - 1799 - 1805 +JF - Phys. Chem. Chem. Phys. +VL - 3 +IS - (10) +N1 - Complex vibrational correlation functions extracted from the resolved 2 band of liquid acetonitrile +ID - 152 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +PY - 2001 +TI - Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM +SP - 1113-1123 +JF - J. Chem. Inf. Comput. Sci. +VL - 41 +N1 - Chemical markup, XML and the World-Wide Web. 2. Information objects and the CMLDOM +ID - 79 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Wright, M. +PY - 2001 +TI - Development of Chemical Markup Language (CML) as a system for handling complex chemical content +SP - 618-634 +JF - New Journal of Chemistry +VL - 25 +N1 - Development of Chemical Markup Language (CML) as a system for handling complex chemical content +ID - 76 +ER - + +TY - JOUR +AU - Mitchell, J. B. O. +AU - Price, S. L. +AU - Leslie, M. +AU - Buttar, D. +AU - Roberts, R. J. +PY - 2001 +TI - Anisotropic repulsion potentials for cyanuric chloride (C3N3Cl3) and their application to modeling the crystal structures of azaaromatic chlorides +SP - 9961-9971 +JF - J. Phys. Chem. A. +VL - 105 +N1 - Anisotropic repulsion potentials for cyanuric chloride (C3N3Cl3) and their application to modeling the crystal structures of azaaromatic chlorides +ID - 74 +ER - + +TY - JOUR +AU - Mitchell, J. B. O. +PY - 2001 +TI - The relationship between the sequence identities of alpha helical proteins in the PDB and the molecular similarities of their ligands +SP - 1617-1622 +JF - J. Chem. Inf. Comput. Sci. +VL - 41 +N1 - The relationship between the sequence identities of alpha helical proteins in the PDB and the molecular similarities of their ligands +ID - 73 +ER - + +TY - JOUR +AU - Mitchell, J. B. O. +PY - 2001 +TI - Review of ‘Virtual Screening for Bioactive Molecules' +SP - 1148-1149 +JF - J. Chem. Soc. +IS - Perkin Trans. 1 +N1 - Review of ‘Virtual Screening for Bioactive Molecules' +N1 - Also Natural Product Reports, 2001, 18, 360 (Editors H. J. Böhm and G. Schneider) +ID - 83 +ER - + +TY - JOUR +AU - Jandu, K. S. +AU - Barrett, V. +AU - Brockwell, M. +AU - Foster, C. +AU - Giles, H. +AU - Glen, R. C. +AU - Hobbs, H. +AU - Cambridge, D. +AU - Honey, A. +AU - Martin, G. R. +AU - Salmon, J. +AU - D. Smith +AU - Woollard, P. +AU - Selwood., D. L. +PY - 2001 +TI - The Discovery of 4991W93 a 5HT1D/1B Receptor Partial Agonist and a +Potent Inhibitor of Electrically Induced Plasma Extravasation. +SP - 681-693 +JF - J. Med. Chem. +VL - 44 +IS - (1) +N1 - The Discovery of 4991W93 a 5HT1D/1B Receptor Partial Agonist and a +Potent Inhibitor of Electrically Induced Plasma Extravasation. +ID - 16 +ER - + +TY - CHAP +AU - Goodman, J. M. +PY - 2001 +BT - Visions of the Future: Chemistry and Life Science +ED - Thompson, J. M. T. +CT - World champion chemists: people versus computers. +PB - Cambridge University Press +N1 - World champion chemists: people versus computers. +ID - 70 +ER - + +TY - JOUR +AU - Gkoutos, G. V. +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Wright, M. +PY - 2001 +TI - Chemical markup, XML and the World-Wide Web. 3. Toward a signed semantic chemical web of trust +SP - 1124-1130 +JF - J. Chem. Inf. Comput. Sci. +VL - 41 +N1 - Chemical markup, XML and the World-Wide Web. 3. Toward a signed semantic chemical web of trust +ID - 80 +ER - + +TY - JOUR +AU - Gkoutos, G. V. +AU - Kenway, P. R. +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Wright, M. +PY - 2001 +TI - A resource for transforming HTML and molfile documents to XML compliant form +JF - Internet Journal of Chemistry +VL - 4 +IS - (5) +N1 - A resource for transforming HTML and molfile documents to XML compliant form +ID - 77 +ER - + +TY - JOUR +AU - Gkouto, G. V. +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Viravaidya, C. +AU - Wright, M. +PY - 2001 +TI - The application of XML languages for integrating molecular resources. +JF - Internet Journal of Chemistry +VL - 4 +IS - (12) +N1 - The application of XML languages for integrating molecular resources. +ID - 82 +ER - + +TY - JOUR +AU - Claridge, T. D. W. +AU - Goodman, J. M. +AU - Moreno, A. +AU - Angus, D. +AU - Barker, S. F. +AU - Taillefumier, C. +AU - Watterson, M. P. +AU - Fleet, G. W. J. +PY - 2001 +TI - 10-Helical conformations in oxetane b-amino acid hexamers +SP - 4251-4255 +JF - Tet. Lett. +VL - 42 +N1 - 10-Helical conformations in oxetane b-amino acid hexamers +ID - 68 +ER - + +TY - JOUR +AU - Chugh, J. K. +AU - Wallace, B. A. +PY - 2001 +TI - Peptaibols: Models for ion channels +SP - 565-570 +JF - Biochemical Society Transactions +VL - 29 +IS - 4 +N1 - Peptaibols: Models for ion channels +ID - 38 +ER - + +TY - JOUR +AU - Chowdhury, S. F. +AU - Lucrezia, R. Di +AU - Guerrero, R. H. +AU - Brun, R. +AU - Goodman, J. M. +AU - Ruiz-Perez, L. M. +AU - Pacanowska, D. G. +AU - Gilbert, I. H. +PY - 2001 +TI - Novel inhibitors of leishmanial dihydrofolate reductase +SP - 977-980 +JF - Bioorganic and Medicinal Chemistry Letters +VL - 11 +N1 - Novel inhibitors of leishmanial dihydrofolate reductase +ID - 71 +ER - + +TY - JOUR +AU - Brodbelt, J. S. +AU - Isbell, J. +AU - Goodman, J. M. +AU - Secor, H. V. +AU - Seeman, J. I. +PY - 2001 +TI - Gas phase versus solution chemistry: on the reversal of regiochemistry of methylation of sp2- and sp3-nitrogens +SP - 6949-6952 +JF - Tet. Lett. +VL - 42 +N1 - Gas phase versus solution chemistry: on the reversal of regiochemistry of methylation of sp2- and sp3-nitrogens +ID - 66 +ER - + +TY - JOUR +AU - Brailsford, T. +AU - Burt, C. +AU - Calder, J. +AU - Davies, M. +AU - Edge, C. +AU - Murray-Rust, P. +AU - Overington, J. +AU - Richardson, C. M. +PY - 2001 +TI - Virtual education for medicinal chemistry: Early experiences in industrial-academic partnership for continuous learning +JF - Internet Journal of Chemistry +VL - 4 +IS - 3 +N1 - Virtual education for medicinal chemistry: Early experiences in industrial-academic partnership for continuous learning +ID - 78 +ER - + +TY - JOUR +AU - Bellenie, B. R. +AU - Goodman, J. M. +PY - 2001 +TI - The stereochemistry of glabrescol +SP - 7477-7479 +JF - Tet. Lett. +VL - 42 +N1 - The stereochemistry of glabrescol +ID - 64 +ER - + +TY - JOUR +AU - Avalos, M. +AU - Babiano, R. +AU - Bravo, J. L. +AU - Cintas, P. +AU - Higes, F. J. +AU - Jimènez, J. L. +AU - Palacios, J. C. +AU - Silva, M. A. +PY - 2001 +TI - Conjugate additions of heteronucleophiles to enones and alkynoates. A benign design functionalization of heteroaromatics. M. Avalos, R. Babiano, J. L. Bravo, P. Cintas, F. J. Higes, J. L. Jimènez, J. C. Palacios and Silva, M. A. Green chemistry 2001, 3, 26-29 +SP - 26-29 +JF - Green chemistry +VL - 3 +N1 - Conjugate additions of heteronucleophiles to enones and alkynoates. A benign design functionalization of heteroaromatics. M. Avalos, R. Babiano, J. L. Bravo, P. Cintas, F. J. Higes, J. L. Jimènez, J. C. Palacios and Silva, M. A. Green chemistry 2001, 3, 26-29 +ID - 63 +ER - + +TY - JOUR +AU - Murray-Rust, P. +AU - Rzepa, H. S. +AU - Wright, M. +AU - Zara, S. +PY - 2000 +TI - A universal approach to web-based chemistry using XML and CML +SP - 1471-1472 +JF - Chem. Comm. +N1 - A universal approach to web-based chemistry using XML and CML +ID - 95 +ER - + +TY - JOUR +AU - Mitchell, J.B.O. +AU - Price, S.L. +PY - 2000 +TI - A Systematic Non-Empirical Method of Deriving Model Intermolecular Potentials for Organic Molecules: Application to Amides +SP - 10958-10971 +JF - J. Phys. Chem. A, +VL - 104 +N1 - A Systematic Non-Empirical Method of Deriving Model Intermolecular Potentials for Organic Molecules: Application to Amides +ID - 84 +ER - + +TY - JOUR +AU - Menzagh, F. +AU - Trujillo, K. A. +AU - Thomsen, W. J. +AU - Whelan, K. T. +AU - Russo, J. F. +AU - Reyes, H. S. +AU - Beeley, N. +AU - Liaw, C. W. +AU - Hodgkin, E. E. +AU - Glen, R. C. +AU - Smith, J. +AU - Behan, D. P. +AU - Chalmers, D. T. +PY - 2000 +TI - Identification of novel selective 5-HT2A inverse agonists as putative +atypical antipsychotic using constitutively activated human 5-HT +receptors, +SP - 1049 +N1 - May 2000 +JF - FASEB journal +VL - 14 +IS - (18) +N1 - Identification of novel selective 5-HT2A inverse agonists as putative +atypical antipsychotic using constitutively activated human 5-HT +receptors, +ID - 15 +ER - + +TY - JOUR +AU - Jones, G. +AU - Willett, P. +AU - Glen, R. C. +PY - 2000 +TI - GASP: Genetic Algorithm Superposition Program, IUL Biotechnology series, ŒPharmacophore perception, development and use in drug design +N1 - GASP: Genetic Algorithm Superposition Program, IUL Biotechnology series, ŒPharmacophore perception, development and use in drug design +N1 - Glen +ID - 14 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 2000 +TI - On the need for multiple lists of chemical information +SP - 33-36 +JF - Molecules +VL - 5 +N1 - On the need for multiple lists of chemical information +ID - 87 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 2000 +TI - Solutions for chemistry: Synthesis of experiment and calculation +SP - 387-398 +JF - Phil. Trans. Roy. Soc. +VL - 358 +N1 - Solutions for chemistry: Synthesis of experiment and calculation +ID - 86 +ER - + +TY - JOUR +AU - Goodman, J. M. +AU - Kirby, P. D. +AU - Haustedt, L. O. +PY - 2000 +TI - Some calculations for organic chemists: boiling point variation, Boltzmann factors and the Eyring equation +SP - 9879-9882 +JF - Tet. Lett. +VL - 41 +N1 - Some calculations for organic chemists: boiling point variation, Boltzmann factors and the Eyring equation +ID - 85 +ER - + +TY - JOUR +AU - Avalos, M. +AU - Babiano, R. +AU - Bravo, J. L. +AU - Cintas, P. +AU - Jimènez, J. L. +AU - Palacios, J. C. +AU - Silva, M. A. +PY - 2000 +TI - Computational studies on the BF3-catalyzed cycloaddition of furan with methyl vinyl ketone: A new look at Lewis acid catalysis +SP - 6613-6619 +JF - J. Org. Chem. +VL - 65 +N1 - Computational studies on the BF3-catalyzed cycloaddition of furan with methyl vinyl ketone: A new look at Lewis acid catalysis +ID - 88 +ER - + +TY - JOUR +AU - Avalos, M. +AU - Babiano, R. +AU - Cintas, P. +AU - Higes, F. J. +AU - Jimènez, J. L. +AU - Palacios, J. C. +AU - Silva, M. A. +PY - 2000 +TI - Diastereoselective cycloadditions of nitroalkenes as an approach to the assembly of the bicyclic nitrogen heterocycles +SP - 1494-1502 +JF - J. Org. Chem. +VL - 64 +N1 - Diastereoselective cycloadditions of nitroalkenes as an approach to the assembly of the bicyclic nitrogen heterocycles +ID - 90 +ER - + +TY - JOUR +AU - Avalos, M. +AU - Babiano, R. +AU - Bravo, J. L. +AU - Cintas, P. +AU - Higes, F. J. +AU - Jimènez, J. L. +AU - Palacios, J. C. +AU - Silva, M. A. +PY - 2000 +TI - Understanding diastereofacial selection in carbohydrate-based domino cycloadditions: semiempirical and DFT calculations +SP - 267-277 +JF - Chem. Eur. J. +VL - 6 +N1 - Understanding diastereofacial selection in carbohydrate-based domino cycloadditions: semiempirical and DFT calculations +ID - 89 +ER - + +TY - JOUR +AU - Zhang, Q. +AU - Hamilton, D. G. +AU - Feeder, N. +AU - Teat, S. J. +AU - Goodman, J. M. +AU - Sanders, J. K. M. +PY - 1999 +TI - Synthesis and post-assembly modification of some functionalised, neutral π-associated [2]catenanes +SP - 897-903 +JF - New Journal Chemistry +VL - 23 +N1 - Synthesis and post-assembly modification of some functionalised, neutral π-associated [2]catenanes +ID - 100 +ER - + +TY - JOUR +AU - Mitchell, J. B. O. +AU - Laskowski, R. A. +AU - Alex, A. +AU - Thornton, J. M. +PY - 1999 +TI - BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential +SP - 1165-1176 +JF - J. Comp. Chem. +VL - 20 +N1 - BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential +ID - 92 +ER - + +TY - JOUR +AU - Mitchell, J. B. O. +AU - Laskowski, R. A. +AU - Alex, A. +AU - Forster, M. J. +AU - Thornton, J. M. +PY - 1999 +TI - BLEEP - Potential of mean force describing protein–ligand interactions: II. calculation of binding energies and comparison with experimental data +SP - 1177-1185 +JF - J. Comp. Chem. +VL - 20 +N1 - BLEEP - Potential of mean force describing protein–ligand interactions: II. calculation of binding energies and comparison with experimental data +ID - 93 +ER - + +TY - JOUR +AU - Mitchell, J. B. O. +AU - Alex, A. +AU - Snarey, M. +PY - 1999 +TI - SATIS: Atom typing from chemical connectivity +SP - 751-757 +JF - J. Chem. Inf. Comput. Sci. +VL - 39 +N1 - SATIS: Atom typing from chemical connectivity +ID - 91 +ER - + +TY - JOUR +AU - Medhi, C. +AU - Mitchell, J. B. O. +AU - Price, S. L. +AU - Tabor, A. B. +PY - 1999 +TI - Electrostatic factors in DNA intercalation +SP - 84-93 +JF - Biopolymers (Nucleic Acid Sciences) +VL - 52 +N1 - Electrostatic factors in DNA intercalation +ID - 94 +ER - + +TY - JOUR +AU - Goodman, J. M. +PY - 1999 +TI - How Do Approximations Affect the Solutions to Kinetic Equations? +SP - 275-277 +JF - J. Chem. Ed. +VL - 76 +N1 - How Do Approximations Affect the Solutions to Kinetic Equations? +ID - 102 +ER - + +TY - JOUR +AU - Goodman, J. M. +AU - Köhler, A-K. +AU - Alderton, S. C. M. +PY - 1999 +TI - Interactive Analysis of Selectivity in Kinetic Resolutions +SP - 8715-8718 +JF - Tet. Lett. +VL - 40 +N1 - Interactive Analysis of Selectivity in Kinetic Resolutions +N1 - Goodman +ID - 98 +ER - + +TY - JOUR +AU - Dominey, A. P. +AU - Goodman, J. M. +PY - 1999 +TI - An Experimental and Theoretical Study of a Bicyclic Acetal Equilibrium +SP - 473-476 +JF - Org. 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R. +AU - Thomson, W. +TI - Small molecule modulators of non-endogenous, constitutively activated human serotonin receptor +VL - US06150393 +N1 - Small molecule modulators of non-endogenous, constitutively activated human serotonin receptor +ID - 97 +ER - + diff --git a/test/test_bibtexparser.py b/test/test_bibtexparser.py index 7f4c9d61..2ad75333 100644 --- a/test/test_bibtexparser.py +++ b/test/test_bibtexparser.py @@ -4,8 +4,8 @@ class TestBibTexParser: def test_01(self): collection = 'testing' sample = open('test/data/sample.bibtex') - parser = BibTexParser() - data, metadata = parser.parse(sample) + parser = BibTexParser(sample) + data, metadata = parser.parse() print data assert data[0]['title'] == 'Visibility to infinity in the hyperbolic plane, despite obstacles' diff --git a/test/test_csvparser.py b/test/test_csvparser.py index 6b8483d8..1d13c491 100644 --- a/test/test_csvparser.py +++ b/test/test_csvparser.py @@ -4,7 +4,7 @@ class TestCSVParser: def test_01(self): collection = 'testing' sample = open('test/data/sample.csv') - parser = CSVParser() - data, metadata = parser.parse(sample) + parser = CSVParser(sample) + data, metadata = parser.parse() assert data[0]['title'] == 'Visibility to infinity in the hyperbolic plane, despite obstacles' diff --git a/test/test_parser.py b/test/test_parser.py index 6b04a3e5..eb146135 100644 --- a/test/test_parser.py +++ b/test/test_parser.py @@ -7,3 +7,15 @@ def test_01(self): data, metadata = ds.parse(bibtex, 'bibtex') assert data[0]['title'] == 'Visibility to infinity in the hyperbolic plane, despite obstacles' + def test_BOM(self): + from cStringIO import StringIO + csv_file = '''"bibtype","citekey","title","author","year","eprint","subject" + "misc","arXiv:0807.3308","Visibility to infinity in the hyperbolic plane, despite obstacles","Itai Benjamini,Johan Jonasson,Oded Schramm,Johan Tykesson","2008","arXiv:0807.3308","sle" +''' + csv_file_with_BOM = '\xef\xbb\xbf' + csv_file + ds = bibserver.parser.Parser() + data1, metadata = ds.parse(StringIO(csv_file), 'csv') + data2, metadata = ds.parse(StringIO(csv_file_with_BOM), 'csv') + assert data1[0]['bibtype'] == data2[0]['bibtype'] + + \ No newline at end of file diff --git a/test/test_risparser.py b/test/test_risparser.py new file mode 100644 index 00000000..1a5097e0 --- /dev/null +++ b/test/test_risparser.py @@ -0,0 +1,13 @@ +from bibserver.parsers.RISParser import RISParser + +class TestRISParser: + def test_01(self): + collection = 'testing' + sample = open('test/data/sample.ris') + parser = RISParser(sample) + data, metadata = parser.parse() + assert len(data) == 240 + assert type(data[0]['title']) is unicode + assert data[0]['title'] == u'Using Workflows to Explore and Optimise Named Entity Recognition for Chemisty' + assert len(data[0]['author']) == 5 + data[0]['author'][0] = {'name': u'Kolluru, B.K.'} \ No newline at end of file