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. 2004 Jul 1;32(Web Server issue):W526-31.
doi: 10.1093/nar/gkh468.

Protein structure prediction and analysis using the Robetta server

David E Kim  1 , Dylan Chivian, David Baker
Affiliations

Protein structure prediction and analysis using the Robetta server

David E Kim et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
Ginzu domain parsing hierarchy and modeling protocol. The query sequence is scanned for matches to known structures and regions that are likely to be domains. Sections that are not covered but are large enough to be a domain (at least 50 residues) are passed on as input for the next step. The order is based on the relative accuracy of each step. Homologous structure searches are performed first, followed by a search against Pfam-A and then parsing based on MSA sequence clusters. Boundaries are assigned so that putative domains without homologous structures are within size limits accessible to the Rosetta de novo protocol. Regions that are homologous to sequences with known structures are used for comparative modeling. Matches to Pfam-A, MSA cluster domains and remaining uncovered regions of sufficient size are subjected to de novo structure prediction. Domain models are assembled into a full model in the last step.
Figure 2
Figure 2
An example of structure prediction results. Screen shot of the top of the web page (A) and the first 6 of 10 structure predictions located at the bottom of the web page (B).
See this image and copyright information in PMC

References

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    1. Rohl C.A. and Baker,D. (2002) De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J. Am. Chem. Soc., 124, 2723–2729. - PubMed
    1. Meiler J. and Baker,D. (2003) Rapid protein fold determination using unassigned NMR data. Proc. Natl Acad. Sci. USA, 100, 15404–15409. - PMC - PubMed
    1. Kortemme T., Kim,D.E. and Baker,D. (2004) Computational alanine scanning of protein–protein interfaces. Sci. STKE, 2004, pl2. - PubMed
    1. Kortemme T. and Baker,D. (2002) A simple physical model for binding energy hot spots in protein–protein complexes. Proc. Natl Acad. Sci. USA, 99, 14116–14121. - PMC - PubMed