DOCK 6: combining techniques to model RNA-small molecule complexes.

By P. Therese Lang, Scott R. Brozell, Eric F. Pettersen, Elaine C. Meng, V. Thomas, Robert C. Rizzo, David A. Case, Thomas L. James, Irwin D. Kuntz. 2009

719 citations recorded by the source corpus.

Subfields: Molecular Biology

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Citations in the corpus

EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction (2022, background): “, 2020), we argue that errors in the ground truth binding pocket conformation heavily affect traditional docking methods that are conditioned on the receptor active site (Lang et al., 2009; Trott & Olson, 2010).”
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment (2011, positive): “Continuous improvement of molecular modeling and docking algorithms andmethodology (Abagyan et al., 1997; Abagyan and Totrov, 1994; Abel et al., 2010; Barth et al., 2009; Bottegoni et al., 2008, 2009; Brylinski and Skolnick, 2008; Case et al., 2005; Cavasotto et al., 2005, 2008; Chen et al., 2003; D”
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.”
Fast Docking on Graphics Processing Units via Ray-Casting (2013, background): “While some methods allow the ligand conformation to vary during docking [9,12,13], others carry out independent docking trajectories using a series of pre-built low-energy ligand conformations (‘‘conformers’’) [7,14,15].”
Molecular Docking: Shifting Paradigms in Drug Discovery (2019, methodology): “In particular, TarFisDock [54] and idTarget [147] enable the screening of a given ligand to a set of proteins available within the PDTD and PDB by using the DOCK [79] and MEDock [153] docking programs, respectively.”
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids (2014, methodology): “We selected 56 RNA-ligand complexes from the original RiboDock [6] and DOCK6 [22] sets to assess the performance of rDock with RNA as the receptor.”
Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review (2012, background): “For example, Lang et al . recently have optimized DOCK 6 for docking small molecules to RNA targets (55) and obtained a success rate of 70% for the ligands with less than seven rotatable bonds at the 2-Å heavy-atom root-mean-squared deviation threshold.”
Latest developments in molecular docking: 2010–2011 in review (2013, background): “4: [169] rigid, ﬁ xed anchor, and ﬂ exible anchor (while keeping the receptor rigid).”
Challenges and advances in computational docking: 2009 in review (2011, methodology): “Kuntz and co-workers (58) have used two implicit solvent scoring functions AMBER/GBSA and AMBER/PBSA, implemented”