title: The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.
abstract: We present an evaluation of our protein-protein docking approach using the ZDOCK and ZRANK algorithms, in combination with structural clustering and filtering, utilizing biological data in Rounds 6-11 of the CAPRI docking experiment. We achieved at least one prediction of acceptable accuracy for five of six targets submitted. In addition, two targets resulted in medium-accuracy predictions. In the new scoring portion of the CAPRI exercise, we were able to attain at least one acceptable prediction for the three targets submitted and achieved three medium-accuracy predictions for Target 26. Scoring was performed using ZRANK, a new algorithm for reranking initial-stage docking predictions using a weighted energy function and no structural refinement. Here we outline a practical and successful docking strategy, given limited prior biological knowledge of the complex to be predicted.
authors.affiliation: Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Wiehe
authors.forename: Brian
authors.initials: B
authors.lastname: Pierce
authors.forename: Wei Wei
authors.initials: WW
authors.lastname: Tong
authors.forename: Howook
authors.initials: H
authors.lastname: Hwang
authors.forename: Julian
authors.initials: J
authors.lastname: Mintseris
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D030562:Databases, Protein; D019281:Dimerization; D023281:Genomics; D008024:Ligands; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software