Novel algorithms for searching conformational space.

D Byrne; J Li; E Platt; B Robson; P Weiner

doi:10.1007/bf00124350

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Novel algorithms for searching conformational space.

D Byrne·J Li·E Platt·B Robson·P Weiner

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Abstract

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.

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Alanine Algorithms Computer Simulation Information Storage and Retrieval Models, Molecular Molecular Conformation Monte Carlo Method Motion Protein Conformation Journal Article

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D Byrne, J Li, E Platt, B Robson, P Weiner. 1994. Novel algorithms for searching conformational space.. https://doi.org/10.1007/bf00124350

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