CRANKITE: A fast polypeptide backbone conformation sampler

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.