PERMOL: Restraint-based protein homology modeling using DYANA or CNS.

Abstract

PERMOL is a new restraint-based program for homology modeling of proteins. Restraints are generated from the information contained in structures of homologous template proteins. Employing the restraints generated by PERMOL, three-dimensional structures are obtained using MD programs such as DYANA or CNS. In contrast to other programs PERMOL is mainly based on the use of dihedral angle information which is optimally suited to preserve the local secondary structure. The global arrangement of these elements is then facilitated by a small number of distance restraints. Using PERMOL homology, models of high quality are obtained. A key advantage of the proposed method is its flexibility, which allows the inclusion of data from other sources, such as experimental restraints and the use of modern molecular dynamics programs to calculate structures.