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

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# 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](http://www.ksrlab.org/pluqin-sqat/)
- [meihonglab.mit.edu](http://meihonglab.mit.edu/software)

## Requirements

- Python 3.4+ or Python 2.7
- GEOS
- GDAL

To install the requirements on a Mac you can use [Homebrew](https://brew.sh):

```bash
    brew install python3
    brew install geos
    brew install gdal
```

You can also satisfy the requirements using the python packages from 
[Anaconda](https://anaconda.org/anaconda/python).

### 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](http://pacsy.nmrfam.wisc.edu). See `pluq/scripts/build_pacsy`
for more information.

## Install

```bash
    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](https://doi.org/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](https://doi.org/10.1109/BIBMW.2012.6470267)

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