ArticleNucleic acids research2015
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Structure-aware artificial intelligence for next-generation drug discovery: from protein-ligand modeling to generative biomolecular design.Briefings in bioinformatics · 2026Review
- Enabling Automatic Generation of Protein-Ligand Complex Data Sets with Atomistic Detail.Journal of chemical information and modeling · 2026Article
- From Latent Manifolds to Targeted Molecular Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework for Family-Based Kinase Ligand Design.Biomolecules · 2026Article
- OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders.PLoS computational biology · 2025Article
- LIGYSIS-web: a resource for the analysis of protein-ligand binding sites.Nucleic acids research · 2025Article
- 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
- AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.International journal of molecular sciences · 2024Article
- Comparative evaluation of methods for the prediction of protein-ligand binding sites.Journal of cheminformatics · 2024Article
- Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures.Journal of cheminformatics · 2024Article
- How Ligands Interact with the Kinase Hinge.ACS medicinal chemistry letters · 2023Article
- PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters.Database : the journal of biological databases and curation · 2023Article
- Molecular docking in organic, inorganic, and hybrid systems: a tutorial review.Monatshefte fur chemie · 2023Review
- Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools.Scientific reports · 2023Article
- RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning.Nucleic acids research · 2023Article
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Methodology of network pharmacology for research on Chinese herbal medicine against COVID-19: A review.Journal of integrative medicine · 2022Review
- Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students.Biomolecules · 2022Review
- Interpretable Machine Learning Models for Molecular Design of Tyrosine Kinase Inhibitors Using Variational Autoencoders and Perturbation-Based Approach of Chemical Space Exploration.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users.
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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.