The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
SwarmDock: a server for flexible protein–protein docking
Abstract
Summary: Protein–protein interactions are central to almost all biological functions, and the atomic details of such interactions can yield insights into the mechanisms that underlie these functions. We present a web server that wraps and extends the SwarmDock flexible protein–protein docking algorithm. After uploading PDB files of the binding partners, the server generates low energy conformations and returns a ranked list of clustered docking poses and their corresponding structures. The user can perform full global docking, or focus on particular residues that are implicated in binding. The server is validated in the CAPRI blind docking experiment, against the most current docking benchmark, and against the ClusPro docking server, the highest performing server currently available. Availability: The server is freely available and can be accessed at: http://bmm.cancerresearchuk.org/%7ESwarmDock/. Contact: Paul.Bates@cancer.org.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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Cites
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
Comeau, S. R., Gatchell, D. W., Vajda, S., & Camacho, C. J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg371 · Cited by 855
Protein–protein docking benchmark version 4.0
Hwang, H., Vreven, T., Janin, J., & Weng, Z. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22830 · Cited by 476
Docking and scoring protein complexes: CAPRI 3rd Edition
Lensink, M. F., Méndez, R., & Wodak, S. J. (2007) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.21804 · Cited by 340
Liu, S., Zhang, C., Zhou, H., & Zhou, Y. (2004) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20019 · Cited by 193
SwarmDock and the Use of Normal Modes in Protein-Protein Docking
Moal, I. H., & Bates, P. A. (2010) · International Journal of Molecular Sciences · doi:10.3390/ijms11103623 · Cited by 158
Self-citationLi, X., Moal, I. H., & Bates, P. A. (2010) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22770 · Cited by 65
Self-citationDesigning coarse grained-and atom based-potentials for protein-protein docking
Tobi, D. (2010) · BMC Structural Biology · doi:10.1186/1472-6807-10-40 · Cited by 39
Cited by
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
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
Pierce, B. G., Wiehe, K., Hwang, H., Kim, B.-H., Vreven, T., & Weng, Z. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu097 · Cited by 1,760
Software for molecular docking: a review
Pagadala, N. S., Syed, K., & Tuszynski, J. (2017) · Biophysical Reviews · doi:10.1007/s12551-016-0247-1 · Cited by 1,522
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms
Gordon, D. E., Hiatt, J., Bouhaddou, M., Rezelj, V. V., Ulferts, S., Braberg, H., Jureka, A. S., Obernier, K., Guo, J. Z., Batra, J., et al. (2020) · Science · doi:10.1126/science.abe9403 · Cited by 747
DockQ: A Quality Measure for Protein-Protein Docking Models
Basu, S., & Wallner, B. (2016) · PLOS ONE · doi:10.1371/journal.pone.0161879 · Cited by 460
Metadata
- Authors
- Torchala, M., Moal, I. H., Chaleil, R. A. G., Fernandez-Recio, J., & Bates, P. A.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-01-23
- Volume
- 29
- Issue
- 6
- Pages
- 807-809
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2140522686
- Cited by
- 285
- References
- 7
- FWCI
- 8.47
- Type
- journal article
- Language
- en
- Open access
- closed
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