The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Protein structure prediction and analysis using the Robetta server
Open accessAbstract
The Robetta server (http://robetta.bakerlab.org) provides automated tools for protein structure prediction and analysis. For structure prediction, sequences submitted to the server are parsed into putative domains and structural models are generated using either comparative modeling or de novo structure prediction methods. If a confident match to a protein of known structure is found using BLAST, PSI-BLAST, FFAS03 or 3D-Jury, it is used as a template for comparative modeling. If no match is found, structure predictions are made using the de novo Rosetta fragment insertion method. Experimental nuclear magnetic resonance (NMR) constraints data can also be submitted with a query sequence for RosettaNMR de novo structure determination. Other current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning. The Rosetta protein design and protein-protein docking methodologies will soon be available through the server as well.
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Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Predicting coiled coils from protein sequences.
Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953
Domain size distributions can predict domain boundaries
Wheelan, S. J., Marchler-Bauer, A., & Bryant, S. H. (2000) · Bioinformatics · doi:10.1093/bioinformatics/16.7.613 · Cited by 182 · cited 1×
“A significant fraction of domains in the PDB (Protein Data Bank) are within this length (18).”
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Cited by
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Wang, S., Sun, S., Li, Z., Zhang, R., & Xu, J. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005324 · Cited by 931
Zhang, C., Freddolino, L., & Zhang, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx366 · Cited by 606
Structure of activated transcription complex Pol II–DSIF–PAF–SPT6
Vos, S. M., Farnung, L., Boehning, M., Wigge, C., Linden, A., Urlaub, H., & Cramer, P. (2018) · Nature · doi:10.1038/s41586-018-0440-4 · Cited by 432
Distance-based protein folding powered by deep learning
Xu, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1821309116 · Cited by 401
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
Metadata
- Authors
- Kim, D. E., Chivian, D., & Baker, D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-07-01
- Volume
- 32
- Issue
- Web Server
- Pages
- W526-W531
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2115167726
- Cited by
- 2,111
- References
- 3
- FWCI
- 12.57
- Type
- journal article
- Language
- en
- Open access
- bronze
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