Novel algorithms for searching conformational space.
The modelling of biological molecules by molecular dynamics is beset by a range of problems. The most important of these is the multiple-minima problem. The deep metastable minima can cause difficulties in proper equilibration of a molecular system and result in the simulated system being trapped in a long-lived metastable state. One way to overcome these problems is to re-engineer the 'Newtonian Rules' in order to more efficiently search conformational space. Re-engineering of the 'Newtonian Rules' implies a redesign of the physical laws arising from them. This is done in various ways by the RUSH, Hybrid Monte Carlo and PEACS algorithms. This paper explores applications of these algorithms, and compares them to a traditional molecular dynamics method.
Proteus Molecular Design Ltd., Macclesfield, Cheshire, U.K.
D
D
Byrne
J
J
Li
E
E
Platt
B
B
Robson
P
P
Weiner
D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry; D000465:Algorithms; D003198:Computer Simulation; D016247:Information Storage and Retrieval; D008958:Models, Molecular; D008968:Molecular Conformation; D009010:Monte Carlo Method; D009038:Motion; D011487:Protein Conformation
C024314:N-acetylalanyl-N-methylamide; D000409:Alanine