Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta
作者： Zhe Zhang , Christina E. M. Schindler , Oliver F. Lange , Martin Zacharias
DOI: 10.1371/JOURNAL.PONE.0125941
关键词:
摘要: 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 proteins including also possible conformational changes the binding partners. In order explore efficiency improvements MC sampling, several enhanced sampling techniques, temperature or Hamiltonian replica exchange well-tempered ensemble approaches, have been combined with method were evaluated on 20 using unbound partner structures. a 2-dimensional scheme (WTE-H-REMC) was identified as most efficient search strategy. Comparison prolonged searches indicates that WTE-H-REMC approach requires approximately 5 times fewer steps identify near native docking compared conventional searches.
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