Fast protein structure prediction using Monte Carlo simulations with modal moves.
Using normal modes to generate torsion space moves in Monte Carlo simulations of peptides and proteins is not a new idea; nevertheless, despite its power it has not received widespread application. We show that such a "Modal Monte Carlo" approach is an efficient tool for ab initio predictions of small-protein structures. We apply this method to the Trp cage, a 20-residue polypeptide designed to fold rapidly into a structure that includes tertiary contacts, despite its short length. We achieve a high-quality ab initio structure prediction in about 2 orders of magnitude less computation time than state of the art molecular dynamics techniques.
Carnevali
Paolo
P
Protein Mechanics Inc., 280 Hope Street, Mountain View, CA 94041, USA. PCarnevali@ProteinMechanics.com
Tóth
Gergely
G
Toubassi
Garrick
G
Meshkat
Siavash N
SN
D003198:Computer Simulation; D008958:Models, Molecular; D009010:Monte Carlo Method; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D011994:Recombinant Proteins / Q000737:chemistry*
D010455:Peptides; D011994:Recombinant Proteins; C476389:TC5b protein, synthetic