Protein structure prediction force fields: Parametrization with quasi-newtonian dynamics
New York, NY
Biochemistry and Biotechnology
Wiley InterScience Backfile Collection 1832-2000
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. Proteins 27:367-384, 1997. © 1997 Wiley-Liss, Inc.
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