Scoring docking models with evolutionary information.
We have developed methods for the extraction of evolutionary information from multiple sequence alignments for use in the study of the evolution of protein interaction networks and in the prediction of protein interaction. For Rounds 3, 4, and 5 of the CAPRI experiment, we used scores derived from the analysis of multiple sequence alignments to submit predictions for 7 of the 12 targets. Our docking models were generated with Hex and GRAMM, but all our predictions were selected using methods based on multiple sequence alignments and on the available experimental evidence. With this approach, we were able to predict acceptable level models for 4 of the targets, and for a fifth target, we located the residues involved in the binding surface. Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases.
Tress
Michael
M
Protein Design Group, CNB-CSIC, Cantoblanco, Madrid, Spain. mtress@cnb.uam.es <mtress@cnb.uam.es>
de Juan
David
D
Graña
Osvaldo
O
Gómez
Manuel J
MJ
Gómez-Puertas
Paulino
P
González
Jose M
JM
López
Gonzalo
G
Valencia
Alfonso
A
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D019281:Dimerization; D019143:Evolution, Molecular; D006801:Humans; D046911:Macromolecular Substances; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D055672:Static Electricity; D040681:Structural Homology, Protein
D046911:Macromolecular Substances