ArticleCommunications chemistry2023
Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15.
Article in Communications chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed.
- PreStoi allows accurate prediction of protein complex stoichiometry by integrating AlphaFold3 and template information.Communications biology · 2026Article
- Highlights of Model Quality Assessment in CASP16.Proteins · 2026Article
- Improving AlphaFold2- and AlphaFold3-Based Protein Complex Structure Prediction With MULTICOM4 in CASP16.Proteins · 2026Article
- Boosting AlphaFold protein tertiary structure prediction through MSA engineering and extensive model sampling and ranking in CASP16.Communications biology · 2025Article
- Modeling Alternative Conformational States in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code?Biomolecules · 2025Review
- An outlook on structural biology after AlphaFold: tools, limits and perspectives.FEBS open bio · 2025Review
- Modification of Non-photochemical Quenching Pathways in the CbioRxiv : the preprint server for biology · 2025Article
- Estimating protein complex model accuracy using graph transformers and pairwise similarity graphs.Bioinformatics advances · 2025Article
- The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction.Biomolecules · 2024Review
- Improving AlphaFold Predicted Contacts for Alpha-Helical Transmembrane Proteins Using Structural Features.International journal of molecular sciences · 2024Article
- Petabase-Scale Homology Search for Structure Prediction.Cold Spring Harbor perspectives in biology · 2024Review
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures.Journal of cheminformatics · 2024Article
- Protein structure accuracy estimation using geometry-complete perceptron networks.Protein science : a publication of the Protein Society · 2024Article
- DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.Bioinformatics (Oxford, England) · 2023Article
- Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15.Communications biology · 2023Article
- Improving AlphaFold predicted contacts in alpha-helical transmembrane proteins structures using structural features.Research square · 2023Article
- Petascale Homology Search for Structure Prediction.bioRxiv : the preprint server for biology · 2023Article
- Enhancing AlphaFold-Multimer-based Protein Complex Structure Prediction with MULTICOM in CASP15.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
- Update of
Authors and funding
6 authors.
Funding
Abstract
Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.
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.