• eXtended Contact Mode Score
  • Installation Dependencies
    • Python 2.7 and pip
    • OpenBabel and Pybel
    • Pkcombu
    • APoc
  • Installation
  • Usage

eXtended Contact Mode Score

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.