Posted March 5th, 2012 by jseco
Sometimes, I've faced the problem to determine the number of contacts between protein residues and a given ligand (which may come from x-ray or docking results).
In most cases it can be done easily with some chemoinformatic package (such as Openbabel or RDKit), but it isn't affordable and productive to install and learn how to use them just to perform such rudimentary analysis. For that reason, I typed a Perl code that taking as input the ligand (.mol2) and a protein (.pdb) computes every distance between heavy ligand atoms and protein side-chain residues. Of course, the script can be modified (is well commented), and uses as internal cutoff the distance of 6 Amstrong to determine if there is such contact.
After the analysis, the program prints out those residues are in/out of the bniding site. The former ones are printed in PDB format, and the later ones in text file format.