ReviewNature protocols2021
A practical guide to large-scale docking.
Review in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 301 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
301 citing papers in PubMed.
- (+)-Trans-Cannabidiol Is an Agonist at Human CBPharmacology research & perspectives · 2026Article
- Chemical language models for early-stage drug discovery: applications, pitfalls, and future directions.Journal of computer-aided molecular design · 2026Review
- Physical priors improve performance of structure-based binding affinity models.bioRxiv : the preprint server for biology · 2026Article
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- Molecular Docking of Natural Products: Critical Appraisal of Current Methodology and Practical Guidelines.Molecules (Basel, Switzerland) · 2026Review
- Robots and Minimal, Physics-Informed Features: A Hybrid Framework for Enzyme Catalysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An extension of jamdock-suite for virtual screening from raw chemical datasets.STAR protocols · 2026Article
- Structure-Informed Prioritization of Phytochemical Antistreptococcal Candidates: Integrated Molecular Docking and In Vitro Proof-of-Concept Validation AgainstCurrent issues in molecular biology · 2026Article
- Artificial intelligence and ultra-high performance computing methods and experiments for drug discovery: virtual screening, deep learning, molecular dynamics simulations, ADMET modelling, and experimental validation.Molecular biomedicine · 2026Review
- Identification of New Anti-Trypanosoma brucei Leads: An Integrated CRK12-Guided Virtual Screen With Experimental Validation.Chemical biology & drug design · 2026Article
- Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations.Journal of chemical theory and computation · 2026Article
- Computational Investigation of Cinnamon Phytochemicals Targeting Key Cancer Signaling Pathways: Molecular Docking, ADMET and Molecular Dynamics Simulations Analysis.Current issues in molecular biology · 2026Article
- Integrative computational-experimental discovery of α-hederin as a multi-mechanistic, low-toxicity antifungal agent targeting Candida albicans CYP51.Journal of advanced research · 2026Article
- An integrated computational strategy for profiling terpenoid for dual-target leads against Klebsiella pneumoniae penicillin-binding protein 3 and beta-lactamase.Molecular diversity · 2026Article
- Integrating modern computational techniques elevates binding mode identification for molecular fragments.Molecular diversity · 2026Article
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- 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
- Rapid and energy-efficient ultra-large library screening for drug discovery on a SpiNNaker2 neuromorphic chip.Communications chemistry · 2026Article
- Prioritizing neuroactive ligands using motif-guided virtual discovery and zebrafish profiling.npj drug discovery · 2026Article
241 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
Structure-based docking screens of large compound libraries have become common in early drug and probe discovery. As computer efficiency has improved and compound libraries have grown, the ability to screen hundreds of millions, and even billions, of compounds has become feasible for modest-sized computer clusters. This allows the rapid and cost-effective exploration and categorization of vast chemical space into a subset enriched with potential hits for a given target. To accomplish this goal at speed, approximations are used that result in undersampling of possible configurations and inaccurate predictions of absolute binding energies. Accordingly, it is important to establish controls, as are common in other fields, to enhance the likelihood of success in spite of these challenges. Here we outline best practices and control docking calculations that help evaluate docking parameters for a given target prior to undertaking a large-scale prospective screen, with exemplification in one particular target, the melatonin receptor, where following this procedure led to direct docking hits with activities in the subnanomolar range. Additional controls are suggested to ensure specific activity for experimentally validated hit compounds. These guidelines should be useful regardless of the docking software used. Docking software described in the outlined protocol (DOCK3.7) is made freely available for academic research to explore new hits for a range of targets.
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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.