Ranking multiple docking solutions based on the conservation of inter-residue contacts

Romina M. Oliva, Anna Vangone, Luigi Cavallo

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.
Original languageEnglish (US)
Pages (from-to)1571-1584
Number of pages14
JournalProteins: Structure, Function, and Bioinformatics
Issue number9
StatePublished - Jun 17 2013

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: Funding: RO has been supported by the Italian MIUR (Ministero dell'Istruzione, dell'Universita e della Ricerca; Grant PRIN2008). RO thanks Dr. Angelo Ciaramella and Dr. Antonino Staiano for helpful discussions.

ASJC Scopus subject areas

  • General Medicine


Dive into the research topics of 'Ranking multiple docking solutions based on the conservation of inter-residue contacts'. Together they form a unique fingerprint.

Cite this