Molecular dynamics simulations and analysis of ABC transporters

Publisher:
Bentham Science Publishers Ltd
Publication Type:
Journal Article
Citation:
Current Computer-Aided Drug Design, 2006, 2 (3), pp. 203 - 214
Issue Date:
2006-01
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The increasingavailability of atomic-level protein derived from X-ray crystallography and NMR spectroscopy, together with advances in computational power, have ushered in a new era of powerful theoretical apporaches to study protein mechanism,s and, by extension, use a computer-aided structural approach to drug design. Calssical molecular dynamics calculations, in which Newton's equations of motion are solved for all atoms in the system, has emerged as an important tool for analysing protein dynamics at physiologically relevant timescales, in ways that are either very difficult or impossible to do experimentally. Indeed, the computer is becoming a kind of virtual microscope that can observe things not observable by any other means. The availability of more sophisticated parallel computer clusters and program suites will lead to simulations thatw ill be capable of examining entire processes such as polypeptide folding pathways and reaction mechanisms. In this review, the incipient applicationof molecular dynamics analysis of ABC (ATP-Binding Cassette) trasporters is surveyed and discussed, with particular relevance to unresolved and controversial issues.
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