Protein folding: Flexible lattice models

Abstract

In the post genomic era a possibility of theoretical prediction of protein structure from sequence of amino acids is one of the most important and challenging goals of molecular biology. High complexity of the problem requires simplification of molecular models and very efficient computational tools. Proposed here model of protein structure, dynamics and interaction scheme assumes a single interaction center per amino acid residue. This highly simplified representation is supplemented by a number of build-in implicit packing rules that enable a reasonable modeling of protein geometry that is compatible with detailed atomic models. Preliminary applications to ab initio protein folding and distant homology comparative modeling are described and discussed.