CRANKITE: A fast polypeptide backbone conformation sampler

doi:10.1186/1751-0473-3-12

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CRANKITE: A fast polypeptide backbone conformation sampler

Alexei A Podtelezhnikov¹^,2 and David L Wild¹^,3

¹Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA

²Department of Physics, Michigan Technological University, Houghton, MI, USA

³Systems Biology Centre, University of Warwick, Coventry, UK

author email corresponding author email

Source Code for Biology and Medicine 2008, 3:12doi:10.1186/1751-0473-3-12


Published:	24 June 2008

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.