The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
The ClusPro web server for protein–protein docking
Open accessAbstract
The ClusPro server (https://cluspro.org) is a widely used tool for protein–protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
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Cites
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
Dominguez, C., Boelens, R., & Bonvin, A. M. J. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja026939x · Cited by 3,187
ZDOCK: An initial‐stage protein‐docking algorithm
Chen, R., Li, L., & Weng, Z. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10389 · Cited by 1,393
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
CAPRI: A Critical Assessment of PRedicted Interactions
Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J. E., Vajda, S., Vakser, I., & Wodak, S. J. (2003) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10381 · Cited by 703
Self-citationDocking, scoring, and affinity prediction in CAPRI
Lensink, M. F., & Wodak, S. J. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24428 · Cited by 249
Docking and scoring protein interactions: CAPRI 2009
Lensink, M. F., & Wodak, S. J. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22818 · Cited by 226
Pilpa, R. M., Robson, S. A., Villareal, V. A., Wong, M. L., Phillips, M., & Clubb, R. T. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m806007200 · Cited by 118
Cited by
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391
Protein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808
Protein-peptide docking: opportunities and challenges
Ciemny, M., Kurcinski, M., Kamel, K., Kolinski, A., Alam, N., Schueler-Furman, O., & Kmiecik, S. (2018) · Drug Discovery Today · doi:10.1016/j.drudis.2018.05.006 · Cited by 306
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning
Gao, M., Nakajima An, D., Parks, J. M., & Skolnick, J. (2022) · Nature Communications · doi:10.1038/s41467-022-29394-2 · Cited by 252
Taftaf, R., Liu, X., Singh, S., Jia, Y., Dashzeveg, N. K., Hoffmann, A. D., El-Shennawy, L., Ramos, E. K., Adorno-Cruz, V., Schuster, E. J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25189-z · Cited by 261
Metadata
- Authors
- Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S.
- Venue
- Nature Protocols
- Published
- 2017-01-12
- Volume
- 12
- Issue
- 2
- Pages
- 255-278
- ISSN
- 1750-2799 (ISSN-L)
- 1754-2189
- OpenAlex
- W2572080171
- Cited by
- 3,310
- References
- 7
- FWCI
- 63.57
- Type
- journal article
- Language
- en
- Open access
- green
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- Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein–protein docking. Nature Protocols. https://doi.org/10.1038/nprot.2016.169
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