Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

By Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson. 1996

Subfields: Computational Chemistry & Drug Discovery

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Chemistry & Drug Discovery

Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “Genetic algorithms (GA) are an interesting application of the stochastic search, which have been successfully used in molecular docking programs such as AutoDock and Gold [34,35].”
Economic-based Distributed Resource Management and Scheduling for Grid Computing (2002, background): “ution on Grid resources during DBC Cost optimization scheduling. 7.6 Related Work Although many researchers have explored the use of parallel computing techniques in molecular docking for drug design [35][118], there are only a few efforts that use the world wide distributed computers for processing”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “Some example are provided by the earlier versions of AutoDock (Goodsell and Olson, 1990; Morris et al., 1996), ICM (Abagyan et al., 1994), QXP (McMartin and Bohacek, 1997), MCDOCK (Liu and Wang, 1999), AutoDock Vina (Trott and Olson, 2010), ROSETTALIGAND (Meiler and Baker, 2006). b. Tabu search…”
Efficient docking of peptides to proteins without prior knowledge of the binding site (2002, methodology): “…protein without any prior knowledge of their location and conformation A parameter set based on the AMBER force field (Cornell et al. 1995) and the possibility of using flexible as well as fixed torsions for the ligands during the docking procedure make AutoDock an appropriate tool for such a test”
Toward prediction of functional protein pockets using blind docking and pocket search algorithms (2011, methodology): “The blind docking (BD) method has been introduced 7,8 as an extension of the use of the very powerful docking engine AutoDock 9,10 for the above-mentioned case 1 where the chemical identity of the ligand is known.”
PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. (2004, unknown): “…re®nement/model-building programs [X-PLOR (BruÈ nger, 1988), CNS (BruÈ nger et al., 1998), REFMAC5 (Murshudov et al., 1997), SHELX (Sheldrick & Schneider, 1997) and O (Jones et al., 1991)] as well as docking programs [AutoDock 2.4/3.0 (Morris et al., 1996, 1998), Hex (Ritchie & Kemp, 2000)].”
Virtual Screening with AutoDock: Theory and Practice (2010, methodology): “The initial applications of AutoDock were in the analysis of binding modes and catalytic properties of protein and nucleic acid complexes [3,4], and a typical study would include results from several dozen docking simulations.”
Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “AutoDock Vina [137] is a new generation docking program developed by Trott & Olson at the Scripps Research Institute, La Jolla, California, following the success of previous AutoDock versions.”
iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis (2011, background): “Most docking programs (e.g. DOCK [5] and AutoDock [6]) only provide docked poses or loosely coupled these steps.”
Using AutoDock for Ligand‐Receptor Docking (2008, methodology): “This unit introduces ligand-protein docking simulations, using the AutoDock suite of programs (Goodsell and Olson, 1990; Morris et al., 1996, 1998; Huey et al., 2007).”
GEMDOCK: A generic evolutionary method for molecular docking (2004, methodology): “Using our previous scoring function(29) with simplified AMBER-based parameters.(45)”