ArticleScientific data2024
PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery.
Article in Scientific data, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Learning Protein-Protein Binding Free Energies from Interface Graphs and Physicochemical Descriptors.ACS physical chemistry Au · 2026Article
- GeoPep: A Geometry-Aware Masked Language Model for Protein-Peptide Binding Site Prediction.Journal of chemical information and modeling · 2026Article
- Hybrid Approach to Protein-Protein Complex Affinity Prediction Based on Language Models and Molecular Dynamics.International journal of molecular sciences · 2026Article
- More protein-ligand data are needed for AlphaFold-like models to enable drug discovery.Current opinion in structural biology · 2026Review
- BindPred: a framework for predicting protein-protein binding affinity from language model embeddings.Bioinformatics (Oxford, England) · 2026Article
- A paired sequence language model for protein-protein interaction modeling.Nature communications · 2026Article
- SARS-CoV-2 NSP8-Derived Peptide Effectively Suppresses the Activity of Helicase NSP13.Computational and structural biotechnology journal · 2026Article
- Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules Versus Therapeutic Peptides.Biology · 2025Review
- SLAE: Strictly Local All-atom Environment for Protein Representation.bioRxiv : the preprint server for biology · 2025Article
- VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data.Acta pharmaceutica Sinica. B · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but there was a scarcity of studies predicting the PPB affinity itself. The major reason is the paucity of open-source dataset with PPB affinity data. To address this gap, the current study introduced a large comprehensive PPB affinity (PPB-Affinity) dataset. The PPB-Affinity dataset contains key information such as crystal structures of protein-protein complexes (with or without protein mutation patterns), PPB affinity, receptor protein chain, ligand protein chain, etc. To the best of our knowledge, this is the largest publicly available PPB affinity dataset, and we believe it will significantly advance drug discovery by streamlining the screening of potential large-molecule drugs. We also developed a deep-learning benchmark model with this dataset to predict the PPB affinity, providing a foundational comparison for the research community.
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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.