ArticleBioinformatics (Oxford, England)2023
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 133 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
133 citing papers in PubMed.
- Evaluating AlphaFold Tools and Related Scoring Functions for Protein-peptide Complex Prediction.Genomics, proteomics & bioinformatics · 2026Article
- TINA: a geometry-aware post-hoc scoring framework for protein-protein interaction.Acta pharmacologica Sinica · 2026Article
- Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition.Molecular systems biology · 2026Article
- Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes.bioRxiv : the preprint server for biology · 2026Article
- Evaluation of methods for AlphaFold-based integrative modeling.bioRxiv : the preprint server for biology · 2026Article
- ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.Journal of molecular biology · 2026Article
- Combining AI Structure Prediction and Integrative Modeling for Nanobody-Antigen Complexes.Journal of chemical information and modeling · 2026Article
- Multimerization of a rationally designed nanobody for enhanced avidity toward Aβ42 oligomers.Protein science : a publication of the Protein Society · 2026Article
- ABAG-Rank: improving model selection of AlphaFold antibody-antigen complexes by learning to rank.Bioinformatics (Oxford, England) · 2026Article
- Article
- Toward a 4D genome annotation of CHO cells for biomanufacturing.Trends in biotechnology · 2026Review
- Bitter taste TAS2R14 and TAS2R46 receptors bound to G proteins: comparison of cryo-EM, AlphaFold, and molecular dynamics structures.European biophysics journal : EBJ · 2026Article
- Interpreting the effects of DNA polymerase variants at the structural level.Molecular oncology · 2026Article
- PeptiVerse: A unified platform for therapeutic peptide property prediction.Nature communications · 2026Article
- Benchmarking AlphaFold and related deep learning approaches for modeling antibody and TCR antigen recognition.bioRxiv : the preprint server for biology · 2026Article
- When can AlphaFold predict the oligomeric states of proteins?Protein science : a publication of the Protein Society · 2026Article
- A broadly conserved gram-positive lipoprotein regulates cell elongation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Incorporating Surfaced-Induced Dissociation Mass Spectrometry Data into an AlphaFold-derived deep learning network improves protein structure prediction.bioRxiv : the preprint server for biology · 2026Article
- A Chromatin Biology Assessment of AlphaFold3.bioRxiv : the preprint server for biology · 2026Article
- Efficient generation of epitope-targeted antibodies with Germinal.Nature biotechnology · 2026Article
73 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationDespite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. However, how well these methods fare on larger complexes is still unclear. Further, evaluation methods of the quality of multimeric complexes are not well established.
resultsWe analysed the performance of AlphaFold-Multimer on a homology-reduced dataset of homo- and heteromeric protein complexes. We highlight the differences between the pairwise and multi-interface evaluation of chains within a multimer. We describe why certain complexes perform well on one metric (e.g. TM-score) but poorly on another (e.g. DockQ). We propose a new score, Predicted DockQ version 2 (pDockQ2), to estimate the quality of each interface in a multimer. Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures. AVAILABILITY AND IMPLEMENTATION: All scripts, models, and data used to perform the analysis in this study are freely available at https://gitlab.com/ElofssonLab/afm-benchmark.
Indexed as
Identifiers
What OpenQuestion holds
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.