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1: Source Code Biol Med. 2008 Jun 24;3:12.Click here to read Click here to read Links

CRANKITE: A fast polypeptide backbone conformation sampler.

Podtelezhnikov AA, Wild DL.

Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA. david_wild@kgi.edu.

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. 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. RESULTS: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length.

PMID: 18577227 [PubMed - in process]

PMCID: PMC2443148