ArticleScience (New York, N.Y.)2024
AlphaFold2 structures guide prospective ligand discovery.
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Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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95citing papers in PubMed
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Who cites it
95 citing papers in PubMed.
- Mechanistic Basis for 5-HTNature communications · 2026Article
- Structure-based design of subtype-selective psychedelic analogs.Nature communications · 2026Article
- Docking-based virtual screening: Past, present, and future.Biophysical journal · 2026Review
- 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
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- Chemical Distance-Based Acceleration of Large Library Docking with ChemSTEP.ACS central science · 2026Article
- Entering the agentic era of AI in drug discovery.Nature chemical biology · 2026Article
- Structure-Affinity Relationship Optimization of SYA16263 Yields New Ligands with Improved Receptor Affinity and Antipsychotic-Like Properties.ACS omega · 2026Article
- Artificial intelligence in drug discovery - what it is, where we stand and the path forward.Nature reviews. Drug discovery · 2026Review
- Modeling the Sensitivity of Large-Scale Virtual Screening to Scoring Function Accuracy, Artifacts, and Library Composition.Journal of chemical information and modeling · 2026Article
- Library Docking for Cannabinoid-2 Receptor Ligands.Journal of medicinal chemistry · 2026Article
- Prioritizing neuroactive ligands using motif-guided virtual discovery and zebrafish profiling.npj drug discovery · 2026Article
- The use of artificial intelligence (AI) in neuropsychiatric drug discovery: current challenges and future directions.Translational psychiatry · 2026Review
- V-SYNTHES2-the next generation tool for structure-based virtual screening of giga-scale chemical spaces.npj drug discovery · 2026Article
- Revisiting Target-Aware de novo Molecular Generation with TarPass: Between Rational Design and Texas Sharpshooter.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Target identification and assessment in the era of AI.Nature reviews. Drug discovery · 2026Review
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Computer-aided structural modeling and drug discovery for G-protein-coupled receptors in the age of artificial intelligence.Current opinion in structural biology · 2026Review
- Elucidating the Structure and Activation Mechanisms of GPCRs Using Modern Computational and AI Tools.Cell biochemistry and biophysics · 2026Review
- The Selectivity Implications of Docking Libraries with Greater and Lesser Similarities to Bio-like Molecules.Journal of medicinal chemistry · 2026Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
21 authors.
Jiankun Lyu *Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.ORCID 0000-0002-0461-5454
Nicholas Kapolka *Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.ORCID 0000-0003-2223-8207
Ryan Gumpper *Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
Assaf Alon *Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0001-8102-5290
Liang Wang *Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94035, USA.ORCID 0000-0002-8868-8449
Manish K JainDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.ORCID 0000-0001-8173-3326
Ximena Barros-ÁlvarezDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94035, USA.ORCID 0000-0001-6678-9436
Kensuke SakamotoDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.ORCID 0000-0003-4488-1244
Yoojoong KimDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
Jeffrey DiBertoDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.ORCID 0000-0002-8227-2071
Kuglae KimDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.ORCID 0000-0001-6660-8738
Isabella S GlennDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.ORCID 0009-0002-6443-1873
Tia A TumminoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.ORCID 0000-0001-9155-820X
Sijie HuangDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
John J IrwinDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.ORCID 0000-0002-1195-6417
Olga O TarkhanovaChemspace LLC, Kyiv 02094, Ukraine.ORCID 0000-0003-1880-2872
Yurii MorozChemspace LLC, Kyiv 02094, Ukraine.ORCID 0000-0001-6073-002X
Georgios SkiniotisDepartment of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94035, USA.ORCID 0000-0003-0238-7846
Andrew C KruseDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0002-1467-1222
Brian K ShoichetDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.ORCID 0000-0002-6098-7367
Bryan L RothDepartment of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.ORCID 0000-0002-0561-6520
Funding
Development and Testing of New Computational Methods for Ligand Discovery and MechanismR35GM122481 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Brian K Shoichet · 2017 to 2026
$8.5MMolecular Details of Psychoactive Drug ActionsR01MH112205 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Bryan L. Roth, Brian K Shoichet · 2017 to 2026
$6.1MMechanistic insights into LSD actions at 5-HT2A serotonin receptorsR37DA045657 · NIDA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Bryan L. Roth · 2018 to 2026
$5.8MSTRUCTURE AND FUNCTION OF MRG-FAMILY RECEPTORSR01DA055656 · NIDA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Bryan L. Roth, Brian K Shoichet · 2022 to 2026
$2.8MUltra-large library docking for ligand discoveryR01GM133836 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI IRWIN, JOHN J. · 2019 to 2022
$1.6MMolecular mechanisms of sigma receptor signalingR01GM119185 · NIGMS · HARVARD MEDICAL SCHOOL · PI KRUSE, ANDREW · 2017 to 2020
$1.3MNIDA NIH HHS R01 DA055656NIDA NIH HHS R37 DA045657NIGMS NIH HHS R01 GM119185NIGMS NIH HHS R01 GM133836NIGMS NIH HHS R35 GM122481NIMH NIH HHS R01 MH112205
Abstract
AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ
Indexed as
Deep LearningDrug DiscoveryMolecular Docking SimulationReceptor, Serotonin, 5-HT2ASerotonin 5-HT2 Receptor AgonistsSerotonin 5-HT2 Receptor AntagonistsCryoelectron MicroscopyDrug DesignHumansLigandsProtein ConformationProtein FoldingReceptors, sigmaSmall Molecule LibrariesLigandsReceptor, Serotonin, 5-HT2AReceptors, sigmaSerotonin 5-HT2 Receptor AgonistsSerotonin 5-HT2 Receptor AntagonistsSmall Molecule Libraries
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