Influence of Stereochemistry in a Local Approach for\nCalculating Protein Conformations

Protein\nstructure prediction is generally based on the use of local\nconformational information coupled with long-range distance restraints.\nSuch restraints can be derived from the knowledge of a template structure\nor the analysis of protein sequence alignment in the framework of\nmodels arising from the physics of disordered systems. The accuracy\nof approaches based on sequence alignment, however, is limited in\nthe case where the number of aligned sequences is small. Here, we\nderive protein conformations using only local conformations knowledge\nby means of the interval Branch-and-Prune algorithm. The computation\nefficiency is directly related to the knowledge of stereochemistry\n(bond angle and ω values) along the protein sequence and, in\nparticular, to the variations of the torsion angle ω. The impact\nof stereochemistry variations is particularly strong in the case of\nprotein topologies defined from numerous long-range restraints, as\nin the case of protein of β secondary structures. The systematic\nenumeration of the conformations improves the efficiency of the calculations.\nThe analysis of DNA codons permits to connect the variations of torsion\nangle ω to the positions of rare DNA codons.