DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases

By Todd J.A Ewing, S. Makino, A. Skillman, A. Skillman, Irwin D. Kuntz. 2001

1,163 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Organic Chemistry, Computational Chemistry & Drug Discovery

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Citations in the corpus

AutoGrow: A Novel Algorithm for Protein Inhibitor Design (2009, background): “AutoDock employs a Lamarckian genetic algorithm that is computationally intensive and time consuming; one study found that Auto-Dock was slower than DOCK, FleX, GOLD, and ICM (58).”
Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand (2015, positive): “…published results of docking algorithms can be challenging for the rapidly evolving hardware, FlexX-PHARM took 26.3 seconds per model in 2002 [4], DOCK took 15 seconds per model in 2001 [3], AutoDock Vina LC took 1 minute per model in 2013 [26], and Glide took 60 seconds per model in 2004 [6].”
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “These approaches are used by ZDOCK [161], MDock [162,163], older versions of DOCK [164], et al. Actually, so-called rigid-body algorithms still consider the ligand flexibility by pre-computing ensembles of putative ligand conformations, followed by rigidly docking each conformation to the protein re”
Protein–ligand docking: Current status and future challenges (2006, background): “Alternative search algorithms are also available.(96) The program encompasses three different scoring functions, none of which contains explicit hydrogen-bonding terms, solvation/ desolvation terms, or hydrophobicity terms, making DOCK a very effective program in fast docking, but with natural limit”
1001 Ways to run AutoDock Vina for virtual screening (2016, methodology): “Currently more than ﬁfty software packages are available for protein-ligand docking, for example AutoDock Vina [3], Glide [4], FlexX [5], GOLD [6], DOCK [7], to name a few.”
Comparative evaluation of eight docking tools for docking and virtual screening accuracy (2004, neutral): “7,15,18,24,39 Benchmarks recently became available for SURFLEX.”