Computer simulation of the receptor-ligand system.
A series of Monte Carlo simulations were carried out for receptor-ligand systems taken from the Protein Data Bank. The models of both objects were based on a simplified low-resolution model. The model chains consisted of alpha carbons and side groups represented by united atoms. The excluded volume effect and specific pairwise contact potential were introduced into the model. The process of docking was simulated step-by-step by random translations and reorientations of the ligand. The stability of complexes formed was investigated for a simple statistical potential between amino acid side groups. The feasibility of the model for finding the binding site on the receptor surface and the proper orientation of docked ligand were also studied.
Romiszowski
Piotr
P
Department of Chemistry, University of Warsaw, 1 Pasteura Str., 02-093 Warsaw, Poland. prom@chem.uw.edu.pl
Sikorski
Andrzej
A
D000465:Algorithms; D003198:Computer Simulation; D008024:Ligands; D008958:Models, Molecular; D009010:Monte Carlo Method; D011506:Proteins / Q000737:chemistry; D011955:Receptors, Drug
D008024:Ligands; D011506:Proteins; D011955:Receptors, Drug