ArticleProteins2020
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.
Article in Proteins, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.PLoS computational biology · 2025Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- The ClusPro AbEMap web server for the prediction of antibody epitopes.Nature protocols · 2023Review
- Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.Nature communications · 2022Article
- In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools.Computers in biology and medicine · 2021Article
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Authors and funding
15 authors.
Funding
Abstract
Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template-based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template-based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https://tbm.cluspro.org, is demonstrated by predicting the protein-protein targets of rounds 38 to 45 of CAPRI.
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Registered trials
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