Prediction of the unknown: inspiring experience with the CAPRI experiment.
We submitted predictions for all seven targets in the CAPRI experiment. For four targets, our submitted models included acceptable, medium accuracy predictions of the structures of the complexes, and for a fifth target we identified the location of the binding site of one of the molecules. We used a weighted-geometric docking algorithm in which contacts involving specified parts of the surfaces of either one or both molecules were up-weighted or down-weighted. The weights were based on available structural and biochemical data or on sequence analyses. The weighted-geometric docking proved very useful for five targets, improving the complementarity scores and the ranks of the nearly correct solutions, as well as their statistical significance. In addition, the weighted-geometric docking promoted formation of clusters of similar solutions, which include more accurate predictions.
Ben-Zeev
Efrat
E
Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
Berchanski
Alexander
A
Heifetz
Alexander
A
Shapira
Boaz
B
Eisenstein
Miriam
M
D000465:Algorithms; D000906:Antibodies / Q000737:chemistry / Q000276:immunology; D000956:Antigens, Viral; D001426:Bacterial Proteins; D001665:Binding Sites; D036022:Capsid Proteins / Q000737:chemistry / Q000276:immunology; D006388:Hemagglutinins / Q000737:chemistry / Q000276:immunology; D046911:Macromolecular Substances; D008958:Models, Molecular; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry / Q000378:metabolism; D025941:Protein Interaction Mapping; D017346:Protein Serine-Threonine Kinases / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D020539:Sequence Analysis, Protein; D000516:alpha-Amylases / Q000737:chemistry / Q000276:immunology
D000906:Antibodies; D000956:Antigens, Viral; D001426:Bacterial Proteins; D036022:Capsid Proteins; D006388:Hemagglutinins; D046911:Macromolecular Substances; D011506:Proteins; C061332:VP6 protein, Rotavirus; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C110847:HPr kinase; D017346:Protein Serine-Threonine Kinases; D000516:alpha-Amylases