articleJournal of Computational ChemistryApr 27, 2015Closed access

DOCK 6: Impact of new features and current docking performance

WJWilliam J. AllenTETrent E. BaliusSMSudipto MukherjeeSRScott R. BrozellDMDemetri Moustakas

Stony Brook University · Rutgers, The State University of New Jersey · +3 more institutions

PubMed
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Abstract

This manuscript presents the latest algorithmic and methodological developments to the structure-based design program DOCK 6.7 focused on an updated internal energy function, new anchor selection control, enhanced minimization options, a footprint similarity scoring function, a symmetry-corrected root-mean-square deviation algorithm, a database filter, and docking forensic tools. An important strategy during development involved use of three orthogonal metrics for assessment and validation: pose reproduction over a large database of 1043 protein-ligand complexes (SB2012 test set), cross-docking to 24 drug-target protein families, and database enrichment using large active and decoy datasets (Directory of…

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Topics & keywords

Topics
Keywords
  • DOCK
  • Docking (animal)
  • Computer science
  • Virtual screening
  • Test set
  • Directory
  • Data mining
  • Bioinformatics
UN Sustainable Development Goals
  • Affordable and clean energy
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