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. Background One important challenge of structural protein modeling is an efficient sampling technique for rapid search through the enormous conformational space [1]. Monte Carlo (MC) simulations, along with molecular dynamics, are among the most commonly used methods of sampling conformational space [2]. Because peptide bonds are rigid and flat, MC simulations are often performed in the ...

• Type: Journal
• Year: 2008
• Where: SCFBM
• Authors: Alexei A. Podtelezhnikov, David L. Wild
• Keywords: Local Crankshaft Rotations, Peptide Bonds, SCFBM 2008, Space