Measure of protein-ligand complex (dis)similarity based on intermolecular contacts
Download the package, unpack the tarball, go to src, and
run make:
$ cd src
$ make cms -f makefileIf successful, the binary cms will show up in bin:
$ ls ../bin
cmsAppend the path of cms to the PATH environment variable
$ 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>$ cd data
$ sh cms.shThe codes have been tested on g++ 4.2.1, but any modern compilers supporting c++ standard libraries should work.
Compare two protein-ligand binding conformations even when they are non-identical systems using eXtended Contact Mode Score (XCMS)
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.
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.
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.
We use Apoc to compare two binding pockets.
You may donwload Apoc program here.
Please add the apoc into your system's PATH variable.
At the command line:
$ pip install xcmsTo install locally only for yourself:
$ pip install xcms --userTo 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.