ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking

Dzmitry Padhorny, Kathryn A. Porter, Mikhail Ignatov, Andrey Alekseenko, Dmitri Beglov, Sergei Kotelnikov, Ryota Ashizawa, Israel Desta, Nawsad Alam, Zhuyezi Sun, Emiliano Brini, Ken Dill, Ora Schueler-Furman, Sandor Vajda, Dima Kozakov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template-based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template-based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https://tbm.cluspro.org, is demonstrated by predicting the protein-protein targets of rounds 38 to 45 of CAPRI.

Original languageAmerican English
Pages (from-to)1082-1090
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Volume88
Issue number8
DOIs
StatePublished - 1 Aug 2020

Bibliographical note

Publisher Copyright:
© 2020 Wiley Periodicals, Inc.

Keywords

  • ambiguous templates
  • docking server
  • homology modeling
  • protein-peptide complexes
  • protein-protein complexes
  • template selection

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