ArticleJournal of molecular biology2015
Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Article in Journal of molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 200 papers.
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200 citing papers in PubMed.
- AlphaFold and Docking Approaches for Antibody-Antigen and Other Targets: Insights From CAPRI Rounds 47-55.Proteins · 2026Article
- TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction.Acta pharmacologica Sinica · 2026Article
- Challenging cases for AlphaFold: two multidomain proteins with zinc-binding-, phosphorylation- or dimerization-driven conformational changes.European biophysics journal : EBJ · 2026Article
- ProteinDock: A physics-informed layer to improve protein-protein docking reliability.bioRxiv : the preprint server for biology · 2026Article
- Hybrid Approach to Protein-Protein Complex Affinity Prediction Based on Language Models and Molecular Dynamics.International journal of molecular sciences · 2026Article
- MD-Transformer: Multimodal Integration of ProtBERT Embeddings and Physicochemical Descriptors for Protein-Protein Interface Residue Prediction.International journal of molecular sciences · 2026Article
- BindPred: a framework for predicting protein-protein binding affinity from language model embeddings.Bioinformatics (Oxford, England) · 2026Article
- Improving protein and protein interactions using pseudo-dimers derived from monomeric proteins.Nature communications · 2026Article
- Interpretable Antibody-Antigen Structural Interface Prediction via Adaptive Graph Learning and Cyclic Transfer.bioRxiv : the preprint server for biology · 2026Article
- IgPose: a generative data-augmented pipeline for robust immunoglobulin-antigen binding prediction.Bioinformatics (Oxford, England) · 2026Article
- Beyond contacts: The important role of the support region in protein complex assembly.Protein science : a publication of the Protein Society · 2026Article
- Article
- Molecular dynamics simulations for understanding dual ubiquitination mechanisms to consider S-phase kinase-associated protein 2 (SKP2) as a potential drug target in breast cancer.Frontiers in chemistry · 2026Article
- Applications and Prospects of Artificial Intelligence in ProteomicsCurrent protein & peptide science · 2026Review
- Can We Extract Physics-like Energies from Generative Protein Diffusion Models?bioRxiv : the preprint server for biology · 2025Article
- Multiscale chiral zeros in biomolecules.Communications chemistry · 2025Article
- Improving B-cell epitope prediction.Drug discovery today · 2025Review
- Integrating diverse experimental information to assist protein complex structure prediction by GRASP.Nature methods · 2025Article
- Increasing the fraction of correct solutions in ensembles of protein-protein docking models by an iterative consensus algorithm.Protein science : a publication of the Protein Society · 2025Article
- Enhancing antibody-antigen interaction prediction with atomic flexibility.PLoS computational biology · 2025Article
140 more citing papers are in PubMed but not listed here.
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12 authors.
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Abstract
We present an updated and integrated version of our widely used protein-protein docking and binding affinity benchmarks. The benchmarks consist of non-redundant, high-quality structures of protein-protein complexes along with the unbound structures of their components. Fifty-five new complexes were added to the docking benchmark, 35 of which have experimentally measured binding affinities. These updated docking and affinity benchmarks now contain 230 and 179 entries, respectively. In particular, the number of antibody-antigen complexes has increased significantly, by 67% and 74% in the docking and affinity benchmarks, respectively. We tested previously developed docking and affinity prediction algorithms on the new cases. Considering only the top 10 docking predictions per benchmark case, a prediction accuracy of 38% is achieved on all 55 cases and up to 50% for the 32 rigid-body cases only. Predicted affinity scores are found to correlate with experimental binding energies up to r=0.52 overall and r=0.72 for the rigid complexes.
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