Exploring the protein landscape in ramachandran space: it's not just psi-phi.
Most methods for the structural comparison of proteins utilize molecular coordinates in the three-dimensional physical space. Recently, a group has presented an elegant novel approach based on the characterization of protein shape in terms of backbone torsion angles. They have demonstrated considerable success in direct comparisons with other techniques, and their method lends itself to rapid screening of structural information from rapidly growing databases. We think that the torsion angle approach can be further strengthened by refining the distance notion that forms the basis of the computational scheme. In particular, we are suggesting to compute the distance along the path that minimizes the transition cost between aligned pairs of angles and therefore likely provides a more meaningful representation of distances between points in Ramachandran space.
Krivan
William
W
Protein Advances, Inc., Seattle, Washington 98104, USA. william.krivan@proteinai.com
Carter
Darrick
D
D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*
D011506:Proteins