ArticleProtein science : a publication of the Protein Society2011
A structure-based benchmark for protein-protein binding affinity.
Article in Protein science : a publication of the Protein Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers, 1 of them a synthesis that pooled it.
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Who cites it
142 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An Experimental Framework for Developing Point-of-Need Biosensors: Connecting Bio-Layer Interferometry and Electrochemical Impedance Spectroscopy.Biosensors · 2022Pooled it
- Learning Protein-Protein Binding Free Energies from Interface Graphs and Physicochemical Descriptors.ACS physical chemistry Au · 2026Article
- Direct interaction between RSV polymerase L and active Rab11a mediates viral ribonucleoprotein transport to assembly sites.PLoS pathogens · 2026Article
- Coupling Far-Western Blotting with Peptide Microarrays Reveals Novel E-Cadherin Spore-Surface Ligands inJournal of proteome research · 2026Article
- A multiscale, Bayesian inference approach to augment mechanistic models of cell signaling with machine-learning predictions of binding affinity.PLoS computational biology · 2026Article
- Computational nanobody design using graph neural networks and Metropolis Monte Carlo sampling.Briefings in bioinformatics · 2026Article
- Protein-protein interactions are a major source of epistasis in genetic interaction networks.Nature communications · 2026Article
- Predicting Protein-Protein Interactions from Machine-Learned Representations.Advances in experimental medicine and biology · 2026Review
- 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
- Thianthrenium Chemistry for Identification of Protein-Protein Interactions in Cells.Journal of the American Chemical Society · 2025Article
- Family with sequence similarity 114 member A1 orchestrates immune evasion in triple-negative breast cancer.Signal transduction and targeted therapy · 2025Article
- Systematic evaluation of predictors for binding free energy changes upon mutations in protein complexes.Briefings in bioinformatics · 2025Article
- Systematic Search for Blood-Brain Barrier Modulating Peptides Based on Exhaustive E-Cadherin Domain-Domain Docking.Journal of chemical information and modeling · 2025Article
- Class 1 Sugar Beet Phytoglobin Shows Strong Affinity to Glyceraldehyde-3-Phosphate Dehydrogenase and DNA In Vitro.International journal of molecular sciences · 2025Article
- MVSF-AB: accurate antibody-antigen binding affinity prediction via multi-view sequence feature learning.Bioinformatics (Oxford, England) · 2025Article
- PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models.BMC bioinformatics · 2025Article
- SNX3 mediates heart failure by interacting with HMGB1 and subsequently facilitating its nuclear-cytoplasmic translocation.Acta pharmacologica Sinica · 2025Article
- Estimating Absolute Protein-Protein Binding Free Energies by a Super Learner Model.Journal of chemical information and modeling · 2025Article
- The impact of curation errors in the PDBBind Database on machine learning predictions of protein-protein binding affinity.Database : the journal of biological databases and curation · 2025Article
- Refined target-mediated drug disposition modeling of the anti-tissue factor pathway inhibitor antibody MG1113 in cynomolgus monkeys and rabbits.Frontiers in pharmacology · 2025Article
82 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
We have assembled a nonredundant set of 144 protein-protein complexes that have high-resolution structures available for both the complexes and their unbound components, and for which dissociation constants have been measured by biophysical methods. The set is diverse in terms of the biological functions it represents, with complexes that involve G-proteins and receptor extracellular domains, as well as antigen/antibody, enzyme/inhibitor, and enzyme/substrate complexes. It is also diverse in terms of the partners' affinity for each other, with K(d) ranging between 10(-5) and 10(-14) M. Nine pairs of entries represent closely related complexes that have a similar structure, but a very different affinity, each pair comprising a cognate and a noncognate assembly. The unbound structures of the component proteins being available, conformation changes can be assessed. They are significant in most of the complexes, and large movements or disorder-to-order transitions are frequently observed. The set may be used to benchmark biophysical models aiming to relate affinity to structure in protein-protein interactions, taking into account the reactants and the conformation changes that accompany the association reaction, instead of just the final product.
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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.