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CRANKITE: a fast polypeptide backbone conformation sampler

By Alexei A. Podtelezhnikov and David L. Wild

Abstract

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details.\ud Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space.\ud Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

Topics: QR
Publisher: BioMed Central Ltd.
Year: 2008
OAI identifier: oai:wrap.warwick.ac.uk:533

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