ArticlePloS one2015
Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Induced fit with replica exchange improves protein complex structure prediction.PLoS computational biology · 2022Article
- Distance-based reconstruction of protein quaternary structures from inter-chain contacts.Proteins · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Article
- Article
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- Classification and prediction of protein-protein interaction interface using machine learning algorithm.Scientific reports · 2021Article
- MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions.ACS omega · 2018Article
- Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.Biophysical journal · 2017Article
- Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.BMC bioinformatics · 2017Article
- Rational design of TNFα binding proteins based on the de novo designed protein DS119.Protein science : a publication of the Protein Society · 2016Article
- GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking.Scientific reports · 2016Article
- Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.Biophysical journal · 2016Article
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4 authors.
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No grant is acknowledged in the PubMed record.
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.
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