Protein folding potential functions

Abstract

There has been a great deal of activity recently on approaches to the calculation of protein folding using specially devised empirical potential functions. We have developed one such function that solves the protein structure recognition problem: given the sequence for a globular protein and a collection of plausible protein conformations, including the native conformation for that sequence, identify the correct, native conformation. Although it has been trained on only 58 single-chain proteins, it recognizes the native conformation for essentially all compact, soluble, globular proteins having known native conformations in comparisons with 10/sup 4/ to 10/sup 6/ reasonable alternative conformations apiece. Furthermore, it correctly discriminates between native and nonnative structures of multichain aggregates without additional information about disulfide bonds or bound ligands. Given its broad successes, we can use it to gain insight into the differences between several seemingly related computational problems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>