ArticleScientific reports2023
Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- MotifLeadDB: A Hierarchical Structural Data Set for Congeneric Ligand Binding Activity Change.Journal of chemical information and modeling · 2026Article
- Enabling Automatic Generation of Protein-Ligand Complex Data Sets with Atomistic Detail.Journal of chemical information and modeling · 2026Article
- Precision fragment addition: domain-specific DeepFrag2 models for smarter lead optimization.Digital discovery · 2026Article
- ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data.Journal of chemical information and modeling · 2026Article
- Decoding the limits of deep learning in molecular docking for drug discovery.Chemical science · 2025Article
- Benchmarking 3D Structure-Based Molecule Generators.Journal of chemical information and modeling · 2025Article
- Machine Learning Meets Physics-based Modeling: A Mass-spring System to Predict Protein-ligand Binding Affinity.Current medicinal chemistry · 2025Review
- Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.PLoS computational biology · 2025Article
- A workflow to create a high-quality protein-ligand binding dataset for training, validation, and prediction tasks.Digital discovery · 2025Article
- Article
- Predicting Inhibition of CDK2 with SAnDReS: The Application of Machine Learning to Navigate the Scoring Function Space.Current medicinal chemistry · 2025Review
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Enzyme function and evolution through the lens of bioinformatics.The Biochemical journal · 2023Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Binding MOAD is a database of protein-ligand complexes and their affinities with many structured relationships across the dataset. The project has been in development for over 20 years, but now, the time has come to bring it to a close. Currently, the database contains 41,409 structures with affinity coverage for 15,223 (37%) complexes. The website BindingMOAD.org provides numerous tools for polypharmacology exploration. Current relationships include links for structures with sequence similarity, 2D ligand similarity, and binding-site similarity. In this last update, we have added 3D ligand similarity using ROCS to identify ligands which may not necessarily be similar in two dimensions but can occupy the same three-dimensional space. For the 20,387 different ligands present in the database, a total of 1,320,511 3D-shape matches between the ligands were added. Examples of the utility of 3D-shape matching in polypharmacology are presented. Finally, plans for future access to the project data are outlined.
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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.