Protein structure prediction and analysis using the Robetta server.
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.
Kim
David E
DE
Structural Genomics of Pathogenic Protozoa, Department of Biochemistry, University of Washington, Seattle WA 98195, USA.
Chivian
Dylan
D
Baker
David
D
D000409:Alanine / Q000235:genetics; D020407:Internet; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
D011506:Proteins; D000409:Alanine