Comparing bound and unbound protein structures using energy calculation and rotamer statistics.
Protein data in the PDB covers only a snapshot of a protein structure. For flexible docking conformational changes need to be considered. Rotamer statistics provide the likelihood for side chain conformations, and further comparison of bound and unbound state yields differences in preferred positions. Furthermore, we do a full sampling of selected chi angles and apply the AMBER force field. Conformation of energy minima complies with the rotamer statistics. Both types of information target the reduction of search space for enumerative docking algorithms and provide parameters for elastic docking.
Koch
Kerstin
K
Technische Fakultät, AG Angewandte Informatik, Universität Bielefeld, Postfach 100131, 33501 Bielefeld, Germany. kerstin@techfak.uni-bielefeld.de
Zöllner
Frank
F
Neumann
Steffen
S
Kummert
Franz
F
Sagerer
Gerhard
G
D030562:Databases, Protein; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
D011506:Proteins