Prediction of CASP6 structures using automated robetta protocols

@article{Chivian2005PredictionOC,
  title={Prediction of CASP6 structures using automated robetta protocols},
  author={Dylan Chivian and David E. Kim and Lars Malmstr{\"o}m and Jack Schonbrun and Carol A. Rohl and David Baker},
  journal={Proteins: Structure},
  year={2005},
  volume={61}
}
The Robetta server and revised automatic protocols were used to predict structures for CASP6 targets. [...] Key Method We incorporated some of the lessons learned in the CASP5 experiment into the server prior to participating in CASP6. We additionally tested new ideas that were amenable to full-automation with an eye toward improving the server. We find that the Robetta server shows the greatest promise for the more challenging targets. The most significant finding from CASP5, that automated protocols can be…Expand
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References

SHOWING 1-10 OF 54 REFERENCES
Protein structure prediction and analysis using the Robetta server
TLDR
The Robetta server provides automated tools for protein structure prediction and analysis and current capabilities include the prediction of the effects of mutations on protein-protein interactions using computational interface alanine scanning. Expand
Automated prediction of CASP‐5 structures using the Robetta server
TLDR
The Robetta server produced quite reasonable predictions for targets in the recent CASP‐5 and CAFASP‐3 experiments, some of which were at the level of the best human predictions. Expand
Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation
TLDR
A fully automated version of the CASP5 protocol produced results that were comparable to the human‐assisted predictions for most of the targets, suggesting that automated genomic‐scale, de novo protein structure prediction may soon be worthwhile. Expand
Rosetta in CASP4: Progress in ab initio protein structure prediction
TLDR
Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous abinitio structure predictions and suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information. Expand
CASP5 assessment of fold recognition target predictions
TLDR
An overview of the fifth round of Critical Assessment of Protein Structure Prediction (CASP5) fold recognition category and discusses a few examples of difficult fold recognition targets to highlight the progress of ab initio‐type methods on difficult structure analogs and the difficulties of predicting multidomain targets and selecting prediction models. Expand
CAFASP3: The third critical assessment of fully automated structure prediction methods
TLDR
The results of the fully automated CAFASP3 experiment, which was carried out in parallel with CASP5, show that significant progress has been achieved in automatic structure prediction and has important implications to the prospects of automated structure modeling in the context of structural genomics. Expand
3D-Jury: A Simple Approach to Improve Protein Structure Predictions
TLDR
The goal for the development of the 3D-Jury system is to create a simple but powerful procedure for generating meta-predictions using variable sets of models obtained from diverse sources to improve the quality of structural annotations of novel proteins. Expand
Protein Structure Prediction Using Rosetta
TLDR
This chapter elaborates protein structure prediction using Rosetta, where short fragments of known proteins are assembled by a Monte Carlo strategy to yield native-like protein conformations. Expand
CAFASP2: The second critical assessment of fully automated structure prediction methods
TLDR
It is expected that in the near future, the performance difference between humans and machines will continue to narrow and that fully automated structure prediction will become an effective companion and complement to experimental structural genomics. Expand
Predictions without templates: New folds, secondary structure, and contacts in CASP5
TLDR
The quality of the best predictions was found to be very good: for nearly every target at least one group predicted a structure close to the correct one, suggesting that the community is moving toward general procedures to predict accurate structures for proteins showing no resemblance to anything seen before. Expand
...
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2
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5
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