Optimized torsion-angle normal modes reproduce conformational changes more accurately than cartesian modes.
We present what to our knowledge is a new method of optimized torsion-angle normal-mode analysis, in which the normal modes move along curved paths in Cartesian space. We show that optimized torsion-angle normal modes reproduce protein conformational changes more accurately than Cartesian normal modes. We also show that orthogonalizing the displacement vectors from torsion-angle normal-mode analysis and projecting them as straight lines in Cartesian space does not lead to better performance than Cartesian normal modes. Clearly, protein motion is more naturally described by curved paths in Cartesian space.
Department of Structural Biology, Stanford Medical School, Stanford, California, USA. jenelle@stanford.edu
Jenelle K
JK
Bray
Dahlia R
DR
Weiss
Michael
M
Levitt
D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D019415:Torque
D011506:Proteins