Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions.

ABSTRACT: Many protein-protein docking algorithms generate numerous possible complex structures with only a few of them resembling the native structure. The major challenge is choosing the near-native structures from the generated set. Recently it has been observed that the density of conserved residue positions is higher at the interface regions of interacting protein surfaces, except for antibody-antigen complexes, where a very low number of conserved positions is observed at the interface regions. In the present study we have used this observation to identify putative interacting regions on the surface of interacting partners. We studied 59 protein complexes, used previously as a benchmark data set for docking investigations. We computed conservation indices of residue positions on the surfaces o

SUBMITTER: Duan Y 

PROVIDER: S-EPMC2253405 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature