The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
ClusPro: a fully automated algorithm for protein-protein docking
Open accessAbstract
ClusPro (http://nrc.bu.edu/cluster) represents the first fully automated, web-based program for the computational docking of protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures, which ClusPro will then download from the PDB server (http://www.rcsb.org/pdb/). The docking algorithms evaluate billions of putative complexes, retaining a preset number with favorable surface complementarities. A filtering method is then applied to this set of structures, selecting those with good electrostatic and desolvation free energies for further clustering. The program output is a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email.
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Citations
Cites
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 · cited 6×
“The scoring function of ZDOCK is more intricate, hence ZDOCK typically has a better ratio of true positives to false positives than using the simpler scoring function of DOT.”
MethodInfluentialPrinciples 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-citation
Cited by
PatchDock and SymmDock: servers for rigid and symmetric docking
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki481 · Cited by 3,018
HexServer: an FFT-based protein docking server powered by graphics processors
Macindoe, G., Mavridis, L., Venkatraman, V., Devignes, M.-D., & Ritchie, D. W. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq311 · Cited by 668
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
Yin, R., Feng, B. Y., Varshney, A., & Pierce, B. G. (2022) · Protein Science · doi:10.1002/pro.4379 · Cited by 335
Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
Yin, R., Feng, B. Y., Varshney, A., & Pierce, B. G. (2021) · doi:10.1101/2021.10.23.465575 · Cited by 335
Cytoplasmic STAT3 represses autophagy by inhibiting PKR activity
Shen, S., Niso-Santano, M., Adjemian, S., Takehara, T., Malik, S. A., Minoux, H., Souquere, S., Mariño, G., Lachkar, S., Senovilla, L., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.09.013 · Cited by 285
Metadata
- Authors
- Comeau, S. R., Gatchell, D. W., Vajda, S., & Camacho, C. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-01
- Volume
- 32
- Issue
- Web Server
- Pages
- W96-W99
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2170421654
- Cited by
- 824
- References
- 3
- FWCI
- 3.61
- Type
- journal article
- Language
- en
- Open access
- bronze
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