Development and validation of a modular, extensible docking program: DOCK 5

By D. Moustakas, P. Therese Lang, S. Pegg, Eric F. Pettersen, Irwin D. Kuntz, N. Brooijmans, Robert C. Rizzo. J. Comput. Aided Mol. Des., 2006

433 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c00709e4c6100be5eb78b7a26373e1576ce91097

How researchers see this paper

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

In Computational Theory and Mathematics

In Molecular Biology

Citations in the corpus

Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “DOCK [39, 141-146] is a successful docking software initially developed by Irwin Kuntz that has been in the market since 1988 and that is available free of charge for academic institutions.”
Computational approaches in target identification and drug discovery (2016, methodology): “Severalsoftware packages are available for docking, such as Gold [94], Autodock [95], AutoDock Vina [96], DOCK [97], GLIDE [98], SURFLEX [99] and others.”
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy (2009, methodology): “40 The DMS program, distributed with DOCK 6.1, was used to generate a molecular surface for each receptor.”
Many-task computing for grids and supercomputers (2008, background): “, astronomy [7, 39], medicine [7, 40, 41], chemistry [42], molecular dynamics [43], and economics [44, 45]) have been run at scales of up to millions of tasks on up to hundreds of thousands of processors.”
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, background): “org/ GA and MC CLIX (Lawrence and Davis, 1992) N/A RBD DARWIN (Taylor and Burnett, 2000) N/A GA DIVALI (Clark and Ajay, 1995) , N/A GA DOCK 6 (Oshiro et al., 1995; Knegtel et al., 1997; Kang et al., 2004; Moustakas et al., 2006) dock.”
DOCK 6: combining techniques to model RNA-small molecule complexes. (2009, methodology): “Hydrogen atoms were positioned to avoid clashes and to form hydrogen bonds where possible; this was done in the presence of bound ligand (Moustakas et al. 2006).”
Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand (2015, positive): “This model is used to guide docking of the ligand, while an Assisted Model Building with Energy Refinement (AMBER) based molecular mechanics force field is used to score the resulting binding positions [7].”
Molecular Docking: Shifting Paradigms in Drug Discovery (2019, background): “According to the obtained in silico results, in particular, the authors demonstrated that the combination of the standard DOCK energy function with an especially devised pharmacophore-based scoring function outperfor ed single approaches in discriminating active from inactive compounds [77].”
Automated Docking Screens: A Feasibility Study (2009, methodology): “GOLD-114 Benchmarking.”
New design strategies for antidepressant drugs (2013, background): “Docking is a computational technique that assists in predicting the binding modes of ligands within the target protein pocket [93].”