Protein structure prediction and analysis using the Robetta server
Top Cited Papers
Open Access
- 1 July 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 32 (Web Server) , W526-W531
- https://doi.org/10.1093/nar/gkh468
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.Keywords
This publication has 38 references indexed in Scilit:
- De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using RosettaJournal of the American Chemical Society, 2002
- The Pfam Protein Families DatabaseNucleic Acids Research, 2002
- Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. CohenJournal of Molecular Biology, 2001
- What is the value added by human intervention in protein structure prediction?Proteins-Structure Function and Bioinformatics, 2001
- Native protein sequences are close to optimal for their structuresProceedings of the National Academy of Sciences, 2000
- MaxSub: an automated measure for the assessment of protein structure prediction qualityBioinformatics, 2000
- Domain size distributions can predict domain boundariesBioinformatics, 2000
- De novo protein structure determination using sparse NMR dataJournal of Biomolecular NMR, 2000
- Comparison of sequence profiles. Strategies for structural predictions using sequence informationProtein Science, 2000
- Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von HeijneJournal of Molecular Biology, 1999