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If you use MOLS 2.0 for publication, please cite :

Paul DS, Gautham N (2016) MOLS 2.0: software package for peptide modeling and protein–ligand docking. J Mol Model 22:1–9. doi: 10.1007/s00894-016-3106-x

Queries/suggestions regarding MOLS 2.0 may be sent to sampaul_d@outlook.com

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MOLS 2.0: Software Package for Peptide Modelling and Protein-Ligand Docking

D. Sam Paul and N. Gautham

Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai 600025. India.

The final publication is available at Springer via http://dx.doi.org/[10.1007/s00894-016-3106-x]

Abstract
We have earlier developed an algorithm to perform conformational searches of proteins and peptides, and to perform docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (MOLS) for rationally sampling the vast conformational (or docking) space, and then analyses this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was programmed as MOLS 1.0. The docking portion of the algorithm, which allows only ‘flexible ligand – rigid receptor’ docking, was programmed as MOLSDOCK. Both are FORTRAN based command-line-only molecular docking computer programs, though a GUI was developed later for MOLS 1.0. Both the conformational search and the ‘rigid receptor’ docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating ‘induced fit’ side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the ‘flexible receptor’ portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both ‘flexible ligand – rigid receptor’ and ‘flexible ligand – flexible receptor’ techniques) more accessible to the research community, we have developed MOLS 2.0, which incorporates a new Java-based Graphical User Interface (GUI). Here we give a detailed description of MOLS 2.0. The source code and binary of MOLS 2.0 are distributed free (under GNU Lesser General Public License) for the scientific community. They are freely available for download at https://sourceforge.net/projects/mols2-0/files/.