1. CRANKITE: A fast polypeptide backbone conformation sampler.
- Author
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Podtelezhnikov, Alexei A. and Wild, David L.
- Subjects
- *
SOFTWARE samplers , *MONTE Carlo method , *POLYPEPTIDES , *PROTEIN conformation , *SIMULATION methods & models - 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. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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