Integrating atom-based and residue-based scoring functions for protein-protein docking

UMMS Affiliation

Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology

Publication Date


Document Type



Algorithms; Protein Binding; Protein Conformation; Proteins


Bioinformatics | Computational Biology | Systems Biology


Most scoring functions for protein-protein docking algorithms are either atom-based or residue-based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom-based terms. Here we combine ZRANK's atom-based potentials with five residue-based potentials published by other labs, as well as an atom-based potential IFACE that we published after ZRANK. We simultaneously optimized the weights for selected combinations of terms in the scoring function, using decoys generated with the protein-protein docking algorithm ZDOCK. We performed rigorous cross validation of the combinations using 96 test cases from a docking benchmark. Judged by the integrative success rate of making 1000 predictions per complex, addition of IFACE and the best residue-based pair potential reduced the number of cases without a correct prediction by 38 and 27% relative to ZDOCK and ZRANK, respectively. Thus combination of residue-based and atom-based potentials into a scoring function can improve performance for protein-protein docking. The resulting scoring function is called IRAD (integration of residue- and atom-based potentials for docking) and is available at http://zlab.umassmed.edu.

DOI of Published Version



Protein Sci. 2011 Sep;20(9):1576-86. doi: 10.1002/pro.687. Epub 2011 Aug 8. Link to article on publisher's site

Journal/Book/Conference Title

Protein science : a publication of the Protein Society

Related Resources

Link to Article in PubMed

PubMed ID