Protein structure prediction and analysis using the Robetta server.

David E Kim; Dylan Chivian; David Baker

doi:10.1093/nar/gkh468

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Protein structure prediction and analysis using the Robetta server.

David E Kim·Dylan Chivian·David Baker

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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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Alanine Internet Models, Molecular Nuclear Magnetic Resonance, Biomolecular Protein Conformation Protein Structure, Tertiary Proteins Reproducibility of Results Sequence Analysis, Protein Software Structural Homology, Protein User-Computer Interface Journal Article

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David E Kim, Dylan Chivian, David Baker. 2004-07-01. Protein structure prediction and analysis using the Robetta server.. https://doi.org/10.1093/nar%2Fgkh468

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