Determination of Interaction Potentials of Amino Acids from Native Protein Structures: Test on Simple Lattice Models

TL;DR

This paper introduces a new method combining optimization and geometry to determine amino acid interaction potentials from native protein structures, tested on lattice models with known interactions, showing high accuracy.

Contribution

The paper presents a novel approach for extracting amino acid interaction potentials using a combined optimization and geometrical method applicable to native structures.

Findings

High agreement between extracted and true potentials on lattice models

Method effective even with limited native structure data

Comparison shows advantages over existing methods

Abstract

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also uncovers the shortcomings of any optimization procedure. The strategy can be applied on any data set of native structures such as those available from the Protein Data Bank (PDB). In this work, however, we explain and test our approach on simple lattice models, where the true interactions are known a priori. Excellent agreement is obtained between the extracted and the true potentials even for modest numbers of protein structures in the PDB. Comparisons with other methods are also discussed.