Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation

By Philip Bradley, Dylan Chivian, Jens Meiler, Kira M. S. Misura, Carol A. Rohl, William R. Schief, W. Wedemeyer, O. Schueler‐Furman, Paul Murphy, J. Schonbrun and 2 more. 2003

188 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

Protein 3D Structure Computed from Evolutionary Sequence Variation (2011, methodology): “A series of ingenious methods have led to significant progress as reported in CASP since then, including threading, molecular dynamics, fragment-based assembly, contact prediction, machine learning, as well as methods combining several techniques [16,63,72,73].”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, neutral): “This seems to suggest that the distance of models to the closest PDB structures may be considered as an indicator of model quality (37).”
3D Protein Structure Predicted from Sequence (2011, unknown): “A series of ingenious methods have led to significant progress as reported in CASP since then, including threading, molecular dynamics, fragment-‐based assembly, contact prediction, machine learning, as well as met”
PEP-FOLD: an online resource for de novo peptide structure prediction (2009, methodology): “The application of the Rosetta approach to peptides remains to be evaluated (7), and all-atom molecular dynamics or Monte Carlo simulations in explicit or implicit solvent models with replica exchanges are hampered by the computer time and resources (8,9).”
Modeling structurally variable regions in homologous proteins with rosetta (2004, unknown): “substantial fragments ( 60 residues) of the query sequence.(32,33)”
Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, methodology): “R O-SETTA has displayed remarkable success in de novo structure prediction in the last several blind CASP experiments; this is evidenced by the method’s ranking among the top structure prediction groups ( 16 , 19 , 22 , 28 - 31 ).”
Protein structure prediction and analysis using the Robetta server (2004, unknown): “The Rosetta method is described in detail in references (7–9) and the use of Rosetta in CASP-5 and CAFASP-3 is described in references (6,7).”
Porter: a new, accurate server for protein secondary structure prediction (2005, methodology): “Accurate SS information has been shown to improve the sensitivity of threading methods (e.g. Jones, 1999b) and is at the core of most ab initio methods (e.g. see Bradley et al., 2003) for the prediction of protein structure.”
Local Protein Structures (2007, methodology): “Rosetta algorithm, de novo protein structure prediction method [14, 338] from Baker's lab has been one of the most successful prediction methods in the CASP experiments [318, 339].”
Multipass membrane protein structure prediction using Rosetta (2005, unknown): “These values are comparable to the accuracy of low-resolution predictions made by the Rosetta method for water-soluble proteins of the same length.(7) The FRAGFOLD method has been recently extended to multipass MEMBRANE PROTEIN STRUCTURE PREDICTION 1023”