ArticleJournal of open source software2024
alchemlyb: the simple alchemistry library.
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Article in Journal of open source software, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16citing papers in PubMed
–field-weighted citation impact
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.
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Who cites it
16 citing papers in PubMed.
- Assessment of the Binding Affinity of Covalent Inhibitors of Cruzain and Cathepsin L Using Relative Binding Free Energy.ChemMedChem · 2026Article
- LignAmb25: A comprehensive AMBER force field addressing lignin's structural and chemical diversity.Biophysical journal · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- Martini 3 Metabolome.Journal of chemical theory and computation · 2026Article
- Assessment and Optimization of Force Fields for Glycine Polymorphism and Solution Properties.Journal of chemical theory and computation · 2026Article
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Fluorescent Marinoquinoline Derivative as Inhibitors ofJournal of medicinal chemistry · 2025Article
- Automated parametrization of small molecules within the Martini 3 coarse-grained model guided by experimental log P values.Scientific reports · 2025Article
- All Roads Lead to Carbinolamine: QM/MM Study of Enzymatic C-N Bond Cleavage in Anaerobic Glycyl Radical Enzyme Choline Trimethylamine-Lyase (CutC).The journal of physical chemistry. B · 2025Article
- Article
- Navigating chemical space: multi-level Bayesian optimization with hierarchical coarse-graining.Chemical science · 2025Article
- Force Switching and Potential Shifting Lead to Significant Cutoff Dependence in Alchemical Free Energies.Journal of chemical theory and computation · 2025Article
- Amino acid transfer free energies reveal thermodynamic driving forces in biomolecular condensate formation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Discovery of Novel Pyridin-2-yl Urea Inhibitors Targeting ASK1 Kinase and Its Binding Mode by Absolute Protein-Ligand Binding Free Energy Calculations.International journal of molecular sciences · 2025Article
- Protocols for Metallo- and Serine-β-Lactamase Free Energy Predictions: Insights from Cross-Class Inhibitors.The journal of physical chemistry. B · 2024Article
- Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation.Nature communications · 2022Article
Corrections and comments
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Authors and funding
18 authors.
Zhiyi WuExscientia plc, Schroedinger Building, Oxford, United Kingdom.ORCID 0000-0002-7615-7851
David L DotsonDepartment of Physics, Arizona State University, Tempe, Arizona, United States of America.ORCID 0000-0001-5879-2942
Irfan AlibayOpen Free Energy, Open Molecular Software Foundation, Davis, California, United States.ORCID 0000-0001-5787-9130
Bryce K AllenDifferentiated Therapeutics, San Diego, CA.ORCID 0000-0002-0804-8127
Mohammad Soroush BarhaghiDepartment of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan, United States of America.ORCID 0000-0001-8226-7347
Jérôme HéninUniversité Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France.ORCID 0000-0003-2540-4098
Thomas T JosephDepartment of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.ORCID 0000-0003-1323-3244
Ian M KenneyDepartment of Physics, Arizona State University, Tempe, Arizona, United States of America.ORCID 0000-0002-9749-8866
Hyungro LeePacific Northwest National Laboratory, Richland, Washington, United States of America.ORCID 0000-0002-4221-7094
Haoxi LiUNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States of America.ORCID 0009-0004-8369-1042
Victoria LimDepartments of Pharmaceutical Sciences and Chemistry, University of California Irvine, Irvine, California, United States of America.ORCID 0000-0002-8632-633X
Shuai LiuSilicon Therapeutics LLC, Boston, United States of America.ORCID 0000-0003-1839-9868
Domenico MarsonMolecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy.ORCID 0000-0003-1839-9868
Pascal T MerzPM Scientific Consulting, Basel, Switzerland.ORCID 0000-0002-7045-8725
Alexander SchlaichStuttgart Center for Simulation Science (SC SimTech) & Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany.ORCID 0000-0002-4250-363X
David MobleyDepartments of Pharmaceutical Sciences and Chemistry, University of California Irvine, Irvine, California, United States of America.ORCID 0000-0002-1083-5533
Michael R ShirtsUniversity of Colorado Boulder, Boulder, Colorado, United States of America.ORCID 0000-0003-3249-1097
Oliver BecksteinDepartment of Physics, Arizona State University, Tempe, Arizona, United States of America.ORCID 0000-0003-1340-0831
Funding
Accelerating drug discovery via ML-guided iterative design and optimizationR35GM148236 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI David Lowell Mobley · 2023 to 2026
$2.2MMolecular mechanisms of secondary active transportersR01GM118772 · NIGMS · ARIZONA STATE UNIVERSITY-TEMPE CAMPUS · PI BECKSTEIN, OLIVER · 2016 to 2020
$1.5MEfficient prediction of transmembrane binding sites for anesthetic ligandsK08GM139031 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI JOSEPH, THOMAS THENGANPALLIL · 2020 to 2024
$984kNIGMS NIH HHS K08 GM139031NIGMS NIH HHS R01 GM118772NIGMS NIH HHS R35 GM148236
Abstract
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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.