The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Principles of flexible protein–protein docking
Open accessAbstract
Treating flexibility in molecular docking is a major challenge in cell biology research. Here we describe the background and the principles of existing flexible protein–protein docking methods, focusing on the algorithms and their rational. We describe how protein flexibility is treated in different stages of the docking process: in the preprocessing stage, rigid and flexible parts are identified and their possible conformations are modeled. This preprocessing provides information for the subsequent docking and refinement stages. In the docking stage, an ensemble of pre‐generated conformations or the identified rigid domains may be docked separately. In the refinement stage, small‐scale movements of the backbone and side‐chains are modeled and the binding orientation is improved by rigid‐body adjustments. For clarity of presentation, we divide the different methods into categories. This should allow the reader to focus on the most suitable method for a particular docking problem. Proteins 2008. Published Wiley‐Liss, Inc.
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The ClusPro web server for protein–protein docking
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Self-citationImproved prediction of protein-protein interactions using AlphaFold2
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Self-citationComputational prediction of protein–protein binding affinities
Siebenmorgen, T., & Zacharias, M. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1448 · Cited by 184
“15,16,25,35 In addition, the de novo design of protein – protein interactions requires docking or modeling of new protein – protein interfaces.”
Background
Metadata
- Authors
- Andrusier, N., Mashiach, E., Nussinov, R., & Wolfson, H. J.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2008-09-03
- Volume
- 73
- Issue
- 2
- Pages
- 271-289
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2152872596
- Cited by
- 225
- References
- 8
- FWCI
- 8.19
- Type
- journal article
- Language
- en
- Open access
- green
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