The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
The RosettaDock server for local protein-protein docking
Open accessAbstract
The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein-protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.
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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 2×
“Several protein–protein docking servers are available on the Internet, including ClusPro (2), GRAMM-X (3) and ZDOCK (4) based on fast-Fourier transform methods for grid matching; PatchDock and SymmDock (5) based on shape complementarity principles and symmetry restrictions; and Hex based on spherical harmonic represen…”
MethodCAPRI: 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
Cited by
CEACAM1 regulates TIM-3-mediated tolerance and exhaustion
Huang, Y.-H., Zhu, C., Kondo, Y., Anderson, A. C., Gandhi, A., Russell, A., Dougan, S. K., Petersen, B.-S., Melum, E., Pertel, T., et al. (2015) · Nature · doi:10.1038/nature13848 · Cited by 717
Predicting Protein–Protein Interactions from the Molecular to the Proteome Level
Keskin, O., Tuncbag, N., & Gursoy, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00683 · Cited by 369
Preza, G. C., Ruchala, P., Pinon, R., Ramos, E., Qiao, B., Peralta, M. A., Sharma, S., Waring, A., Ganz, T., & Nemeth, E. (2011) · Journal of Clinical Investigation · doi:10.1172/jci57693 · Cited by 234
PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes
Zaidman, D., Prilusky, J., & London, N. (2020) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.0c00589 · Cited by 224
RosettaAntibody: antibody variable region homology modeling server
Sircar, A., Kim, E. T., & Gray, J. J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp387 · Cited by 161
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Metadata
- Authors
- Lyskov, S., & Gray, J. J.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-05-19
- Volume
- 36
- Issue
- Web Server
- Pages
- W233-W238
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2019691413
- Cited by
- 592
- References
- 2
- FWCI
- 7.32
- Type
- journal article
- Language
- en
- Open access
- gold
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