Protein structure prediction force fields: parametrization with quasi-newtonian dynamics.
We present an unusual method for parametrizing low-resolution force fields of the type used for protein structure prediction. Force field parameters were determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space. The quasi-energy term favored folded native structures and specifically penalized folded nonnative structures. The force field was generated after optimizing less than 70 adjustable parameters, but shows a strong ability to discriminate between native structures and compact misfolded alternatives. The functional form of the force field was chosen as in molecular mechanics and is not table-driven. It is continuous with continuous derivatives and is thus suitable for use with algorithms such as energy minimization or newtonian dynamics.
Ulrich
P
P
Computational Chemistry (Physical Chemistry) ETH Zentrum, Zürich, Switzerland.
Scott
W
W
van Gunsteren
W F
WF
Torda
A E
AE
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins