Application of enhanced sampling Monte Carlo methods for high-resolution protein-protein docking in Rosetta

Zhe Zhang, Christina E.M. Schindler, Oliver F. Lange, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

21 Scopus citations

Abstract

The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches.

Original languageEnglish
Article numbere0125941
JournalPLoS ONE
Volume10
Issue number6
DOIs
StatePublished - 8 Jun 2015
Externally publishedYes

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