ArticlePloS one2013
Ligand pose and orientational sampling in molecular docking.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed.
- γ-glutamyl carboxylase inhibition by Anisindione.Structure (London, England : 1993) · 2026Article
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Small-Molecule Activators of PRMT1: Discovery, SAR Analyses, and Proapoptotic Effects in Pancreatic Cancer Cells.Journal of medicinal chemistry · 2026Article
- Small molecule inhibitor of orphan GPCR dimerization improves host defense and blood pressure control in mice.The Journal of clinical investigation · 2026Article
- Modeling the Sensitivity of Large-Scale Virtual Screening to Scoring Function Accuracy, Artifacts, and Library Composition.Journal of chemical information and modeling · 2026Article
- Docking of virtual libraries identifies small-molecule agonists of neurotensin receptors with analgesic activity.Nature communications · 2026Article
- DOCKweb: a web-based GUI platform for molecular modeling with DOCK6.Journal of computer-aided molecular design · 2026Article
- Benchmarking docking and ML re-scoring screening performance for KRAS G12D in pancreatic cancer.Molecular diversity · 2026Article
- Improving AlphaFold2 Performance in Virtual Screens Targeting GPCRs by Enhancing Binding-Site Conformational Sampling.Journal of chemical information and modeling · 2026Article
- Quantum computing applications in drug discovery.Briefings in bioinformatics · 2026Review
- Article
- Expanding the Palette of Molecular Fragments for Small Molecule De Novo Design Through Isosteric Swapping.Journal of computational chemistry · 2026Article
- Identification of potent high-affinity secondary nucleation inhibitors of Aβ42 aggregation from an ultra-large chemical library using deep docking.Molecular systems biology · 2026Article
- In silico docking yields small molecule negative allosteric modulators targeting the core of Frizzled 7.Nature communications · 2025Article
- Ultra-large virtual screening unveils potent agonists of the neuromodulatory orphan receptor GPR139.Nature communications · 2025Article
- Integrative network pharmacology and molecular dynamics analysis ofRSC advances · 2025Article
- Protein Structural Model Selection Informed by Comparison of Predicted Ligand Binding Poses.Journal of chemical information and modeling · 2025Article
- CarsiDock-Cov: A deep learning-guided approach for automated covalent docking and screening.Acta pharmaceutica Sinica. B · 2025Article
- Hierarchical AF2RAVE for Multiconformation Virtual Screening Targeting S100 CaJournal of chemical theory and computation · 2025Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys-Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20,000 molecular orientations in the binding site (and so from about 1×10(10) to 4×10(10) to 1×10(11) to 2×10(11) to 5×10(11) mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.