pluq
Python tools for analyzing the PACSY NMR chemical shift database and assigning protein chemical shifts.
The main goal of this project is to provide methods for evaluating protein chemical shift data against a large database of assigned chemical shifts, see Ref[1].
We have performed a statistical analysis of the chemical shifts in the PACSY database, Ref [2] which contains >3000 proteins with 3D structures. After removal of misreferenced and misassigned data we have determined refined (multidimensional) chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.). These chemical shift ranges can be used to gain amino-acid type-assignment and/or secondary-structure information from experimental NMR spectra.
You can find related software and some examples on Klaus Schmidt-Rohr's and Mei Hong's lab websites:
Requirements
- Python 3.4+ or Python 2.7
- GEOS
- GDAL
To install the requirements on a Mac you can use Homebrew:
brew install python3
brew install geos
brew install gdal
You can also satisfy the requirements using the python packages from Anaconda.
Optional Requirements
To use the chemical shift assignment program pluqin
discussed in Ref. [1]
you do not need to install the whole PACSY database.
If however you would like to run piqc
or use pluq
to make PACSY database
queries, etc. you will need to have MySQL
installed (or another SQL database
server system). You will also need to download the data from the
PACSY website. See pluq/scripts/build_pacsy
for more information.
Install
cd <path/to/pluq>/pluq
pip3 install -r requirements.txt
python3 setup.py install
If you would like to run piqc
or use pluq
to make PACSY database
queries, etc. you will also need to have the python package MySQLdb
or
mysqlclient
installed. If you have installed Python 2.7, you will need
MySQLdb
. If you have Python 3.4+ installed you will need to the package
mysqlclient
.
References
If you find this package useful in your work please cite these two papers.
- K. J. Fritzsching, Mei Hong, K. Schmidt-Rohr. "Conformationally Selective Multidimensional Chemical Shift Ranges in Proteins from a PACSY Database Purged Using Intrinsic Quality Criteria " J. Biomol. NMR 2016, 64 (2), 115–130 doi:10.1007/s10858-016-0013-5
- Lee, W.; Yu, W.; Kim, S.; Chang, I.; Lee, W. PACSY, a Relational Database Management System for Protein Structure and Chemical Shift Analysis. J Biomol NMR 2012, 54 (2),169–179. doi:10.1109/BIBMW.2012.6470267