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

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

2003-01-31

arxiv.org/abs/cond-mat/0302002v1

Physics

Condensed Matter

Soft Condensed Matter

22 pages, 7 figures, and 5 tables

Scientific paper

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.

Affiliated with

Also associated with

No associations

Rating

On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-390755