PROTEIN-STRUCTURE PREDICTION FORCE-FIELDS - PARAMETRIZATION WITH QUASI-NEWTONIAN DYNAMICS

We present an unusual method for parametrizing low-resolution force fi elds of the type used for protein structure prediction, Force field pa rameters were determined by assigning each a fictitious mass and using a quasi-molecular dynamics algorithm in parameter space, The quasi-en ergy term favored folded native structures and specifically penalized folded nonnative structures, The force field was generated after optim izing less than 70 adjustable parameters, but shows a strong ability t o discriminate between native structures and compact misfolded alterna tives, The functional form of the force field was chosen as in molecul ar mechanics and is not table-driven, It is continuous with continuous derivatives and is thus suitable for use with algorithms such as ener gy minimization or newtonian dynamics. (C) 1997 Wiley-Liss, Inc.