Journal
BIOTECHNOLOGY ADVANCES
Volume 33, Issue 6, Pages 1130-1140Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.biotechadv.2014.11.011
Keywords
Molecular dynamics simulation; Alchemistic simulations; Parallel tempering; Metadynamics; Free energy surface; Drug design
Categories
Funding
- Czech Ministry of Education, Youth and Sport via COST action GLISTEN [CM1207, LD14133]
- Czech Ministry of Education, Youth and Sport via COST action MultiGlycoNano [CM1102, LD13024]
- Czech Ministry of Education, Youth and Sport via specific university research [20/2014]
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Biomolecular simulations are routinely used in biochemistry and molecular biology research; however, they often fail to match expectations of their impact on pharmaceutical and biotech industry. This is caused by the fact that a vast amount of computer time is required to simulate short episodes from the life of biomolecules. Several approaches have been developed to overcome this obstacle, including application of massively parallel and special purpose computers or non-conventional hardware. Methodological approaches are represented by coarse-grained models and enhanced sampling techniques. These techniques can show how the studied system behaves in long time-scales on the basis of relatively short simulations. This review presents an overview of new simulation approaches, the theory behind enhanced sampling methods and success stories of their applications with a direct impact on biotechnology or drug design. (C) 2014 Elsevier Inc. All rights reserved.
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