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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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 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
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Predicting Protein–Protein Interactions from the Molecular to the Proteome Level
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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
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Sircar, A., Kim, E. T., & Gray, J. J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp387 · Cited by 161
Self-citationHot-spot analysis for drug discovery targeting protein-protein interactions
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Bai, N., Riching, K. M., Makaju, A., Wu, H., Acker, T. M., Ou, S.-C., Zhang, Y., Shen, X., Bulloch, D. N., Rui, H., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101653 · Cited by 77
Premkumar, L., Bobkov, A. A., Patel, M., Jaroszewski, L., Bankston, L. A., Stec, B., Vuori, K., Côté, J.-F., & Liddington, R. C. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.102517 · Cited by 68
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Refinement of protein-protein complexes in contact map space with metadynamics simulations
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Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts
Soltanikazemi, E., Quadir, F., Roy, R. S., Guo, Z., & Cheng, J. (2022) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26269 · Cited by 15
Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints
Christoffer, C., Harini, K., Archit, G., & Kihara, D. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168486 · Cited by 4
Jaiswal, A., Roy, R., Tamrakar, A., Singh, A. K., Kar, P., & Kodgire, P. (2023) · Scientific Reports · doi:10.1038/s41598-023-46448-7 · Cited by 3
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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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
