On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design

TL;DR

This paper introduces a novel nonlinear kernel potential for protein folding and design, outperforming traditional linear potentials by effectively discriminating native structures and sequences using a geometric optimization framework.

Contribution

It develops a new framework for designing nonlinear protein potentials using Gaussian kernels, improving discrimination of native proteins over existing linear methods.

Findings

Nonlinear kernel potentials achieve perfect discrimination of native structures.

Linear potentials cannot perfectly discriminate native sequences in complex tasks.

Nonlinear potentials perform well on independent test sets.

Abstract

Potential functions are critical for computational studies of protein structure prediction, folding, and sequence design. A class of widely used potentials for coarse grained models of proteins are contact potentials in the form of weighted linear sum of pairwise contacts. However, these potentials have been shown to be unsuitable choices because they cannot stabilize native proteins against a large number of decoys generated by gapless threading. We develop an alternative framework for designing protein potential. We describe how finding optimal protein potential can be understood from two geometric viewpoints, and we derive nonlinear potentials using mixture of Gaussian kernel functions for folding and design. The optimization criterion for obtaining parameters of the potential is to minimize bounds on the generalization error of discriminating protein structures and decoys not used in training. In our experiment we use a training set of 440 protein structures repre senting a major portion of all known protein structures, and about 14 million structure decoys and sequence decoys obtained by gapless threading. We succeeded in obtaining nonlinear potential with perfect discrimination of the 440 native structures and native sequences. For the more challenging task of sequence design when decoys are obtained by gapless threading, we show that there is no linear potential with perfect discrimination of all 440 native sequences. Results on an independent test set of 194 proteins also showed that nonlinear kernel potential performs well.