ArticleProteins2023
Tertiary structure assessment at CASP15.
Article in Proteins, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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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.
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Who cites it
34 citing papers in PubMed, 47 citations in OpenAlex.
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- Rapidly evolving aphid gall effector proteins exhibit saposin-like folds.bioRxiv : the preprint server for biology · 2026Article
- Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction.Proteins · 2026Article
- Comparative evaluation of the prediction accuracy of AlphaFold and ESMFold for monomeric and dimeric proteins.NAR genomics and bioinformatics · 2026Article
- CASP16 Protein Monomer Structure Prediction Assessment.Proteins · 2026Article
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
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- Building a continuous benchmarking ecosystem in bioinformatics.PLoS computational biology · 2025Article
- Modeling protein conformational ensembles by guiding AlphaFold2 with Double Electron Electron Resonance (DEER) distance distributions.Nature communications · 2025Article
- EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologs.bioRxiv : the preprint server for biology · 2025Article
- Recent progress and future challenges in structure-based protein-protein interaction prediction.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Decoding the functional impact of the cancer genome through protein-protein interactions.Nature reviews. Cancer · 2025Review
- SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations.Genomics, proteomics & bioinformatics · 2025Article
- Comprehensive assessment of AlphaFold's predictions of secondary structure and solvent accessibility at the amino acid-level in eukaryotic, bacterial and archaeal proteins.Computational and structural biotechnology journal · 2025Article
- AlphaFold 2, but not AlphaFold 3, predicts confident but unrealistic β-solenoid structures for repeat proteins.Computational and structural biotechnology journal · 2025Article
- ABCFold: easier running and comparison of AlphaFold 3, Boltz-1, and Chai-1.Bioinformatics advances · 2025Article
- Recent advances and challenges in protein complex model accuracy estimation.Computational and structural biotechnology journal · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
The results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing the outstanding performance of AlphaFold 2 (AF2) at CASP14, all single-chain predictions were assessed together, irrespective of whether a template was available. At CASP15, there was no single stand-out group, with most of the best-scoring groups-led by PEZYFoldings, UM-TBM, and Yang Server-employing AF2 in one way or another. Many top groups paid special attention to generating deep Multiple Sequence Alignments (MSAs) and testing variant MSAs, thereby allowing them to successfully address some of the hardest targets. Such difficult targets, as well as lacking templates, were typically proteins with few homologues. Local divergence between prediction and target correlated with localization at crystal lattice or chain interfaces, and with regions exhibiting high B-factor factors in crystal structure targets, and should not necessarily be considered as representing error in the prediction. However, analysis of exposed and buried side chain accuracy showed room for improvement even in the latter. Nevertheless, a majority of groups produced high-quality predictions for most targets, which are valuable for experimental structure determination, functional analysis, and many other tasks across biology. These include those applying methods similar to those used to generate major resources such as the AlphaFold Protein Structure Database and the ESM Metagenomic atlas: the confidence estimates of the former were also notably accurate.
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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.