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@manual{mpmath,
key = {mpmath},
author = {Fredrik Johansson and others},
title = {mpmath: a {P}ython library for arbitrary-precision floating-point arithmetic (version 0.14)},
note = {{\tt http://code.google.com/p/mpmath/}},
month = {February},
year = {2010},
}
@article{Waldispuhl2008,
author = {Waldisp\"{u}hl, J\'{e}r\^{o}me and Devadas, Srinivas and Berger, Bonnie and Clote, Peter},
doi = {10.1371/journal.pcbi.1000124},
file = {:Users/zenon/Documents/Mendeley/Waldisp\"{u}hl et al/2008/PLoS Computational Biology/Waldisp\"{u}hl et al.\_2008\_Efficient Algorithms for Probing the RNA Mutation Landscape.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Computational Biology},
number = {8},
pages = {e1000124},
title = {{Efficient Algorithms for Probing the RNA Mutation Landscape}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1000124},
volume = {4},
year = {2008}
}
Automatically generated by Mendeley 1.6
Any changes to this file will be lost if it is regenerated by Mendeley.
@article{Turner2010,
abstract = {The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. The initial release covers parameters for predicting RNA folding free energy and enthalpy changes.},
author = {Turner, Douglas H and Mathews, David H},
doi = {10.1093/nar/gkp892},
file = {:Users/zenon/Documents/Mendeley/Turner, Mathews/2010/Nucleic acids research/Turner, Mathews\_2010\_NNDB the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Algorithms,Base Sequence,Computational Biology,Computational Biology: methods,Computational Biology: trends,Databases, Genetic,Databases, Nucleic Acid,Information Storage and Retrieval,Information Storage and Retrieval: methods,Internet,Molecular Sequence Data,Nucleic Acid Conformation,Nucleic Acid Denaturation,RNA,RNA: chemistry,Software,Thermodynamics},
month = jan,
number = {Database issue},
pages = {D280--2},
pmid = {19880381},
title = {{NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2808915\&tool=pmcentrez\&rendertype=abstract},
volume = {38},
year = {2010}
}
Automatically generated by Mendeley 1.6
Any changes to this file will be lost if it is regenerated by Mendeley.
@article{Stombaugh2009,
abstract = {Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson-Crick base pairs play a central role. Non-Watson-Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can potentially occur in conserved motifs. We extract and classify base pairs from a reduced-redundancy set of RNA 3D structures from the Protein Data Bank (PDB) and calculate centroids (exemplars) for each base combination and geometric base pair type (family). We use the exemplars and IDI values to update our online Basepair Catalog and the Isostericity Matrices (IM) for each base pair family. From the database of base pairs observed in 3D structures we derive base pair occurrence frequencies for each of the 12 geometric base pair families. In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments.},
author = {Stombaugh, Jesse and Zirbel, Craig L and Westhof, Eric and Leontis, Neocles B},
doi = {10.1093/nar/gkp011},
file = {:Users/zenon/Documents/Mendeley/Stombaugh et al/2009/Nucleic acids research/Stombaugh et al.\_2009\_Frequency and isostericity of RNA base pairs(2).pdf:pdf},
issn = {1362-4962},
journal = {Nucleic acids research},
keywords = {Base Pairing,Base Sequence,Models, Molecular,Nucleic Acid Conformation,RNA,RNA, Bacterial,RNA, Bacterial: chemistry,RNA, Ribosomal,RNA, Ribosomal: chemistry,RNA: chemistry,Sequence Alignment,Sequence Analysis, RNA},
month = apr,
number = {7},
pages = {2294--312},
pmid = {19240142},
title = {{Frequency and isostericity of RNA base pairs.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19240142},
volume = {37},
year = {2009}
}
Automatically generated by Mendeley 1.6
Any changes to this file will be lost if it is regenerated by Mendeley.
@article{Lari1990,
author = {Lari, K and Young, SJ},
doi = {10.1016/0885-2308(90)90022-X},
file = {:Users/zenon/Documents/Mendeley/Lari, Young/1990/Computer Speech \& Language/Lari, Young\_1990\_The estimation of stochastic context-free grammars using the Inside-Outside algorithm.pdf:pdf},
issn = {08852308},
journal = {Computer Speech \& Language},
month = jan,
number = {1},
pages = {35--56},
title = {{The estimation of stochastic context-free grammars using the Inside-Outside algorithm}},
url = {http://www.sciencedirect.com/science/article/pii/088523089090022X http://linkinghub.elsevier.com/retrieve/pii/088523089090022X},
volume = {4},
year = {1990}
}
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