An interval-based algorithm to represent conformational states of experimentally determined polypeptide templates and fast prediction of approximated 3D protein structures

Abstract

Predicting the three-dimensional (3-D) structure of a protein that has no templates in the Protein Data Bank (PDB) is a very hard, still an impossible task. Computational prediction methods have been developed during the last years, but the problem still remains challenging. In this paper we present a new strategy based on Interval Arithmetic to store structural information obtained from experimental protein templates and predict native-like approximate three-dimensional structures of proteins. Our objective is to perform the prediction in a very fast manner and predict native-like structures that can be used as starting point structures to ab initio methods. We illustrate the efficacy of our method in five case studies of polypeptides.