jyarger/pluq

Python tools for analyzing the PACSY NMR chemical shift database and assigning protein chemical shifts

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:

• ksrlab.org
• meihonglab.mit.edu

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.

1. 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
2. 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