GReMLIN

GReMLIN is a scalable graph based strategy which models protein-ligand interfaces as graphs.

1. Prerequisites

• Python 3x (requiriments.txt)
• java 1.7.0
• openbabel v2.3.1
• Chemaxon

2. Run GReMLIN

GReMLIN uses PMapper, a Chemaxon program to percieve pharmacophoric properties of atoms of given ligands. You could include the Chemaxon software by moving the Chemaxon folder to GReMLIN/config/.

The program is run by the python script called "gremlin.py". To use GReMLIN, simply type "python3 gremlin.py", using the parameters -d followed by the name of a directory contaning many PDB valid files, and -o followed by the name of a output directory to save the results, as shown below

python3 gemlin.py -d datesets/ricin/ -o outputDir/

3. Results

Given the output directory, GReMLIN generates another directories containing the results, as shown below:

Output directories:

• receptor/

directory containing .pdb files slpitted by chain

• ligands/

directory containing ligands files extracted from .pdb structures

• graphs/

directory containing .graphs files in json format with interaction information

• groups/

directory containing files in gspan format grouped by properties similarity.

• patterns/

directory containing graph patterns found in each group in json format.

• supports/

directory containing graphs grouped by support.