ParDOCK: an all atom energy based Monte Carlo docking protocol for protein-ligand complexes.
We report here an all-atom energy based Monte Carlo docking procedure tested on a dataset of 226 protein-ligand complexes. Average root mean square deviation (RMSD) from crystal conformation was observed to be approximately 0.53 A. The correlation coefficient (r(2)) for the predicted binding free energies calculated using the docked structures against experimental binding affinities was 0.72. The docking protocol is web-enabled as a free software at www.scfbio-iitd.res.in/dock.
Gupta
A
A
Department of Chemistry & Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
Gandhimathi
A
A
Sharma
P
P
Jayaram
B
B
D001499:Bayes Theorem; D008024:Ligands; D009010:Monte Carlo Method; D011494:Protein Kinases / Q000378:metabolism; D011506:Proteins / Q000378:metabolism*
D008024:Ligands; D011506:Proteins; D011494:Protein Kinases