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Zhang, Z.* ; Lange, O.F.

Replica exchange improves sampling in low-resolution docking stage of RosettaDock.

PLoS ONE 8:e72096 (2013)
Publ. Version/Full Text Volltext DOI PMC
Open Access Gold
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Many protein-protein docking protocols are based on a shotgun approach, in which thousands of independent random-start trajectories minimize the rigid-body degrees of freedom. Another strategy is enumerative sampling as used in ZDOCK. Here, we introduce an alternative strategy, ReplicaDock, using a small number of long trajectories of temperature replica exchange. We compare replica exchange sampling as low-resolution stage of RosettaDock with RosettaDock's original shotgun sampling as well as with ZDOCK. A benchmark of 30 complexes starting from structures of the unbound binding partners shows improved performance for ReplicaDock and ZDOCK when compared to shotgun sampling at equal or less computational expense. ReplicaDock and ZDOCK consistently reach lower energies and generate significantly more near-native conformations than shotgun sampling. Accordingly, they both improve typical metrics of prediction quality of complex structures after refinement. Additionally, the refined ReplicaDock ensembles reach significantly lower interface energies and many previously hidden features of the docking energy landscape become visible when ReplicaDock is applied.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Protein-protein Docking ; Parallel Tempering Simulations ; Biomolecular Complexes ; Molecular-dynamics ; Prediction ; Capri ; Conformations ; Optimization ; Displacement ; Performance
ISSN (print) / ISBN 1932-6203
Journal PLoS ONE
Quellenangaben Volume: 8, Issue: 8, Pages: , Article Number: e72096 Supplement: ,
Publisher Public Library of Science (PLoS)
Publishing Place Lawrence, Kan.
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Structural Biology (STB)