ArticleProteins2019
Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking.
Article in Proteins, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Diversity, Distribution and Structural Prediction of the Pathogenic Bacterial Effectors EspN and EspS.Genes · 2024Article
- Integrative modeling of guanylate binding protein dimers.Protein science : a publication of the Protein Society · 2023Article
- Article
- The ClusPro AbEMap web server for the prediction of antibody epitopes.Nature protocols · 2023Review
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Article
- Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.Nature communications · 2022Article
- Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches.International journal of molecular sciences · 2021Review
- Performance and Its Limits in Rigid Body Protein-Protein Docking.Structure (London, England : 1993) · 2020Article
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.Proteins · 2020Article
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
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Authors and funding
14 authors.
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Abstract
As a participant in the joint CASP13-CAPRI46 assessment, the ClusPro server debuted its new template-based modeling functionality. The addition of this feature, called ClusPro TBM, was motivated by the previous CASP-CAPRI assessments and by the proven ability of template-based methods to produce higher-quality models, provided templates are available. In prior assessments, ClusPro submissions consisted of models that were produced via free docking of pre-generated homology models. This method was successful in terms of the number of acceptable predictions across targets; however, analysis of results showed that purely template-based methods produced a substantially higher number of medium-quality models for targets for which there were good templates available. The addition of template-based modeling has expanded ClusPro's ability to produce higher accuracy predictions, primarily for homomeric but also for some heteromeric targets. Here we review the newest additions to the ClusPro web server and discuss examples of CASP-CAPRI targets that continue to drive further development. We also describe ongoing work not yet implemented in the server. This includes the development of methods to improve template-based models and the use of co-evolutionary information for data-assisted free docking.
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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.