PERMOL: restraint-based protein homology modeling using DYANA or CNS

PERMOL: restraint-based protein homology modeling using DYANA or CNS

SUMMARY 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 i...

Probabilistic protein homology modeling

Discrete restraint-based protein modeling and the C -trace problem

We present a novel de novo method to generate protein models from sparse, discretized restraints on the conformation of the main chain and side chain atoms. We focus on C -trace generation, the problem of constructing an accurate and complete model from approximate knowledge of the positions of the C atoms and, in some cases, the side chain centroids. Spatial restraints on the C atoms and side ...

Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles.

Customary practice in predicting 3D structures of protein-protein complexes is employment of various docking methods when the structures of separate monomers are known a priori. The alternative approach, i.e. the template-based prediction with pure sequence information as a starting point, is still considered as being inferior mostly due to presumption that the pool of available structures of p...

Xylanase homology modeling using the inverse protein folding approach.

Xylanase has been used in wood pulp bleaching in an effort to reduce chlorine release into the environment and pollution associated with paper production. The three-dimensional structure of xylanase is important to enable better understanding of the enzyme mechanism and to help design a more thermostable xylanase mutant. At the time this work was begun, there was no sequence homologous protein ...