ArticleProteins2019
Evaluation of template-based modeling in CASP13.
Article in Proteins, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- AI-driven insights into protein misfolding and innate immunity in neurodegenerative diseases.Frontiers in immunology · 2026Review
- Model Quality Assessment for CASP16.Proteins · 2026Article
- Template-based RNA structure prediction advanced through a blind code competition.bioRxiv : the preprint server for biology · 2025Article
- Three-Dimensional Modeling ofAntibodies (Basel, Switzerland) · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- Tertiary structure assessment at CASP15.Proteins · 2023Article
- DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function.Bioinformatics (Oxford, England) · 2023Article
- Assessment of the Performances of the Protein Modeling Techniques Participating in CASP15 Using a Structure-Based Functional Site Prediction Approach: ResiRole.Bioengineering (Basel, Switzerland) · 2023Article
- Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Putting AlphaFold models to work with phenix.process_predicted_model and ISOLDE.Acta crystallographica. Section D, Structural biology · 2022Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- MrParse: finding homologues in the PDB and the EBI AlphaFold database for molecular replacement and more.Acta crystallographica. Section D, Structural biology · 2022Article
- Implications of AlphaFold2 for crystallographic phasing by molecular replacement.Acta crystallographica. Section D, Structural biology · 2022Review
- The chemistry of snake venom and its medicinal potential.Nature reviews. Chemistry · 2022Review
- The crystal structure of vaccinia virus protein E2 and perspectives on the prediction of novel viral protein folds.The Journal of general virology · 2022Article
- Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14).Proteins · 2021Article
- Article
- Modeling SARS-CoV-2 proteins in the CASP-commons experiment.Proteins · 2021Article
- Current Approaches in Supersecondary Structures Investigation.International journal of molecular sciences · 2021Review
- Deep Learning-Based Advances in Protein Structure Prediction.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Performance in the template-based modeling (TBM) category of CASP13 is assessed here, using a variety of metrics. Performance of the predictor groups that participated is ranked using the primary ranking score that was developed by the assessors for CASP12. This reveals that the best results are obtained by groups that include contact predictions or inter-residue distance predictions derived from deep multiple sequence alignments. In cases where there is a good homolog in the wwPDB (TBM-easy category), the best results are obtained by modifying a template. However, for cases with poorer homologs (TBM-hard), very good results can be obtained without using an explicit template, by deep learning algorithms trained on the wwPDB. Alternative metrics are introduced, to allow testing of aspects of structural models that are not addressed by traditional CASP metrics. These include comparisons to the main-chain and side-chain torsion angles of the target, and the utility of models for solving crystal structures by the molecular replacement method. The alternative metrics are poorly correlated with the traditional metrics, and it is proposed that modeling has reached a sufficient level of maturity that the best models should be expected to satisfy this wider range of criteria.
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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.