ecnmr is a python script that exploits evolutionary couplings to extract interface residues in protein homo-multimers from NMR-derived ambiguous contact lists
ecnmr aims to extract a list of interface residues that can be provided as ambiguous interaction restraints in protein-protein docking. Four input files are needed: the PDB file of the monomeric protein, one (or more) lists of evolutionary couplings (ECs), the list of NMR-derived ambiguous contacts in CYANA format and the naccess rsa file with the per-residue solvent accessibility of the monomeric protein. There are two tunable parameters: a distance cutoff below which intra-monomeric contacts are removed and a probability cutoff below with the ECs are not taken in account. The script works on all the platforms supporting python2.7 and can be downloaded from GitHub.
The ecnmr package requires only a standard computer with enough RAM to support the in-memory operations.
ecnmr requires python2.7 and Naccess. Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB file. It can be downloaded for free by researchers at academic and non profit-making institutions from http://wolf.bms.umist.ac.uk/naccess/
The script can work on all the platforms and has been tested on the following systems:
- macOS: El Capitan (10.11.6), Mojave (10.14.1)
- Linux: Ubuntu 18.04
ecnmr depends on the following Python modules:
- re
- numpy
- string
- argparse
The stand-alone ecnmr script can be downloaded from GitHub
git clone https://github.com/davidesala/ecnmr
Detailed instructions to run ecnmr.py can be obtained by typing
python ecnmr.py -h
Expected output
List of matched interface residues:
Res1
Res2
Res3
...
...
Percentage of solvent accessible area represented by the list of residues:
###%
Expected run time on a normal desktop
less than a minute
To run the script on your data
python ecnmr.py [-h] -m PDBFILE -l ECFILE -e CYANAFILE -s NACCESSFILE (rsa format) [-d DIST_VALUE] [-p PROB_VALUE]
To reproduce the results reported in the manuscript on the L-asparaginase II (for P=0.25) type
python ecnmr.py -m '6EOK.pdb' -l 'gremlin.rr.txt' -l 'raptorx.rr.txt' -l 'respre.rr.txt' -e 'cyana_ss.upl' -s '6EOK.rsa' -d 12.0 -p 0.25
To reproduce the results reported in the manuscript on the L-asparaginase II (for P=0.20) type
python ecnmr.py -m '3ECU.pdb' -l 'gremlin.rr.txt' -l 'raptorx.rr.txt' -l 'respre.rr.txt' -e 'cyana_ss.upl' -s '3ECU.rsa' -d 12.0 -p 0.20
To reproduce the results reported in the manuscript on the Sod1 type
python ecnmr.py -m '3ECU.pdb' -l 'gremlin.rr.txt' -l 'raptorx.rr.txt' -l 'respre.rr.txt' -e 'cyana_sol.upl' -s '3ECU.rsa' -d 12.0 -p 0.30
This project is covered under the MIT License.