Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI
Open accessAbstract
The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28-36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed. Proteins 2017; 85:391-398. © 2016 Wiley Periodicals, Inc.
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Despite significant progress, the local refinement problem remains a challenge, especially in cases of conformational changes in the backbone.
“However, despite significant progress in this direction [26–29], the problem remains a challenge, especially in cases of conformational changes in the backbone.”
From Challenges in protein docking (2020) · cites this paper as [27]
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- Authors
- Schindler, C. E. M., Chauvot de Beauchêne, I., de Vries, S. J., & Zacharias, M.
- Affiliations
- Center for Integrated Protein Science Munich (DE)
- Physics Department T38 Technische Universität München Garching 85748 Germany
- Corresponding author
- Zacharias, Martin
- Venue
- Proteins Structure Function and Bioinformatics
- Publisher
- Wiley
- Published
- 2016-11-24
- Volume
- 85
- Issue
- 3
- Pages
- 391-398
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2556787714
- Cited by
- 20
- References
- 50
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2021: 1 · 2020: 6 · 2019: 7 · 2018: 1 · 2017: 2
- FWCI
- 1.73
- Type
- journal article
- Language
- en
- Open access
- green
- hal.science
- Licence
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- DFG, Center for Integrated Protein Science Munich
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- protein-protein docking, protein-peptide docking, Capri, protein complex structure prediction, molecular dynamics refinement, template-based modeling, nucleosome, docking scoring, protein flexibility
- MeSH terms
- Algorithms, Amino Acid Sequence, Binding Sites, Peptides, Protein Binding, Protein Conformation, Proteins, Research Design, Software, Computational Biology, Benchmarking, Protein Interaction Mapping, Structural Homology, Protein, Molecular Docking Simulation
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