Jay W. Ponder

TL;DR: The chapter focuses on a general description of the force fields that are most commonly used at present and gives an indication of the directions of current research that may yield better functions in the near future.

TL;DR: The preliminary tests reported here make it appear likely that templates prepared from the currently known core structures will be able to discriminate between these structures, and an algorithm to supply a list of permitted sequences of internal residues compatible with a known core structure is developed.

TL;DR: In this paper, a new classical empirical potential is proposed for water, which uses a polarizable atomic multipole description of electrostatic interactions, and a modified version of Thole's interaction model is used to damp induction at short range.

TL;DR: It is shown that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions.

TL;DR: In this paper, a variant of the Truncated Newton nonlinear optimization procedure is proposed for potential energy minimization of large molecular systems, which shows particular promise for large molecular system.