Contact Mode Score (CMS)

Measure of protein-ligand complex (dis)similarity based on intermolecular contacts

Installation

Download the package, unpack the tarball, go to src, and run make:

$ cd src
$ make cms -f makefile

If successful, the binary cms will show up in bin:

$ ls ../bin
cms

Append the path of cms to the PATH environment variable

Usage 

$ cms -h
Usage: cms [options] files...

Note that multiple options may follow a hyphen delimiter in a single token,
-cr is equivalent with -c -r

Options:

-h, --help      display this help and exit
-c, --cms       calculate contact mode score
-r, --rmsd      calculate rmsd between two ligands
-f, --frac      calculate fraction of non-specific contacts

To calculate contact mode score, use:
cms -c --lig1 <first ligand> --prt1 <first protein>  --lig2 <second ligand> --prt2 <second protein>

To calculate rmsd, use:
cms -r --lig1 <first ligand> --lig2 <second ligand>

To calculate fraction of non-specific contacts, 
PLEASE USE NATIVE ligand and NATIVE protein for the arguments of lig1 and prt1:
cms -f --lig1 <native ligand> --prt1 <native protein>  --lig2 <second ligand> --prt2 <second protein>

Examples 

$ cd data
$ sh cms.sh

Dependencies

The codes have been tested on g++ 4.2.1, but any modern compilers supporting c++ standard libraries should work.

eXtended Contact Mode Score (XCMS)

Compare two protein-ligand binding conformations even when they are non-identical systems using eXtended Contact Mode Score (XCMS)

Installation Dependencies

Python 2.7 and pip

It is recommended to install Anaconda on your system to set up the python working environment, which provides most of the python dependencies to run XCMS, except for Pybel, whose installation shall be explained below.

OpenBabel and Pybel

We use OpenBabel and its python binding pybel to handle various input formats.

See here for the instructions how you can compile OpenBabel together with its python binding.

Be aware, you must use the old Eigen2 instead of Eigen3.

Pkcombu

We use pkcombu in the KCOMBU package to compare two ligands.

You may download the KCOMBU program here.

Please add the pkcombu into your system's PATH variable.

APoc

We use Apoc to compare two binding pockets.

You may donwload Apoc program here.

Please add the apoc into your system's PATH variable.

Installation

At the command line:

$ pip install xcms

To install locally only for yourself:

$ pip install xcms --user

Usage

To use it:

$ x-cms --help
Usage: x-cms [OPTIONS]

calculated extended contact mode score provided the query and template
protein-ligand structures

Options:
  --template-protein PATH  template protein file path, in PDB format
  --query-protein PATH     query protein file path, in PDB format
  --query-ligand PATH      query ligand file path, in SDF format
  --template-ligand PATH   template ligand file path, in SDF format
  --help                   Show this message and exit.