(page number not for citation purposes) Chemistry Central Journal Open AccessPoster presentation A distance-based method for evaluating protein-structures

The ab initio prediction of a protein's 3D-structure from its amino acid sequence remains an unsolved problem in bioinformatics. While the backbone conformation is dependent on phi- and psi-torsion angles, the formation of secondary and tertiary structure in proteins is based on non-covalent amino acid – amino acid-interactions and the conformations of their side chains. Every non-cova-lent interaction like van der Waals interaction or hydro-gen bonding, between two arbitrary atoms leads to an optimal distance. One can assume that a folded protein is formed by maximizing either the number of non-covalent interactions or, as in this approach, the number of opti-mal distances. A distance-based method was developed. Therefore the atom pair nonhydrogen distances including side chains o