ArticlePLoS computational biology2014
rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 261 papers.
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Who cites it
261 citing papers in PubMed.
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- Fragment-Based Discovery of KLK6 and KLK7 Inhibitors.Journal of chemical information and modeling · 2026Article
- Probe-Atom Distributions Obtained from Mixed-Solvent Molecular Dynamics Improve the Scoring of Docking Calculations.Journal of chemical information and modeling · 2026Article
- Data driven selection of consensus docking pipelines for structure based hit identification.npj drug discovery · 2026Article
- Discovery of novel anti-RSC advances · 2026Article
- Novel Benzofuranyl Chalcones With Antileishmanial Activity: Synthesis, Structure-Activity Relationships, and Computational Target Hypothesis Studies.ChemMedChem · 2026Article
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- Benchmarking Docking Protocols on Predicting Alternative Binding Modes.Journal of chemical information and modeling · 2026Article
- Bridging between Structure-Based and Data-Driven Affinity Prediction.Journal of chemical information and modeling · 2026Article
- Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects.Biochemistry · 2026Article
- Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform.Nature protocols · 2026Review
- Riboswitch-targeted improvement of lysine production in Bacillus and Priestia species.NPJ science of food · 2026Article
- Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.Journal of chemical information and modeling · 2026Article
- An aerosolized dual-action autotaxin inhibitor-PPARγ agonist for the treatment of pulmonary fibrosis.Cell reports. Medicine · 2026Article
- An integrated experimental and computational pipeline for crystallographic fragment screening of membrane protein in the lipid cubic phase.Communications chemistry · 2026Article
- Interplay of RNA mFASEB bioAdvances · 2026Article
- SAFR: Enabling Fragment-Based Drug Discovery with a Synthetic Binding Pose Data Set.Journal of chemical information and modeling · 2026Article
- Development of Small-Molecule Allosteric Modulators of Beta-Galactosidase (β-Gal) for the Treatment of GM1 Gangliosidosis and Morquio B.International journal of molecular sciences · 2026Article
- Synthesis and Biological Profiling of New 1,2,3,4-Tetrahydrobenzo[Biomolecules · 2026Article
201 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
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Abstract
Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrödinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/
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