Skip to main content
Article thumbnail
Location of Repository

CRANKITE: a fast polypeptide backbone conformation sampler

By Alexei A. Podtelezhnikov and David L. Wild


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

Topics: QR
Publisher: BioMed Central Ltd.
Year: 2008
OAI identifier:

Suggested articles


  1. (1968). Are there pathways for protein folding?
  2. (2005). DL: Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds. Proteins-Structure Function and Bioinformatics doi
  3. (2007). DL: Learning about protein hydrogen bonding by minimizing contrastive divergence. Proteins doi
  4. (2005). Efficient Monte Carlo trial moves for polypeptide simulations. doi
  5. (1991). FrankKamenetskii MD:
  6. (1998). GL: Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr doi
  7. (1996). Knapp EW: Protein dynamics with off-lattice Monte Carlo moves. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics doi
  8. (1995). Local moves: an efficient algorithm for simulation of protein folding. Proteins doi
  9. Markov chain Monte Carlo maximum likelihood: ; New York. Edited by: Keramidas EM.
  10. Molecular modelling : principles and applications. 2nd edition.
  11. (1995). Monte Carlo and molecular dynamics simulations in polymer science. doi
  12. (2004). Reduced models of proteins and their applications. Polymer doi
  13. (1999). Scheraga HA: Exact analytical loop closure in proteins using polynomial equations. doi
  14. (1970). Scheraga HA: Ring closure and local conformational deformations of chain molecules. Macromolecules doi
  15. (1993). Theodorou DN: A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses. Molecular Physics doi
  16. (1983). Theoretical studies of protein folding. Annu Rev Biophys Bioeng doi
  17. (2000). Vologodskii A: Multimerization-cyclization of DNA fragments as a method of conformational analysis. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.