Assessment of CASP7 structure predictions for template free targets

@article{Jauch2007AssessmentOC,
  title={Assessment of CASP7 structure predictions for template free targets},
  author={Ralf Jauch and Hock Chuan Yeo and Prasanna R. Kolatkar and Neil D. Clarke},
  journal={Proteins: Structure},
  year={2007},
  volume={69}
}
In CASP7, protein structure prediction targets that lacked substantial similarity to a protein in the PDB at the time of assessment were considered to be free modeling targets (FM). We assessed predictions for 14 FM targets as well as four other targets that were deemed to be on the borderline between FM targets and template based modeling targets (TBM/FM). GDT_TS was used as one measure of model quality. Model quality was also assessed by visual inspection. Visual inspection was performed by… Expand
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References

SHOWING 1-9 OF 9 REFERENCES
Assessment of CASP6 predictions for new and nearly new fold targets
TLDR
The assessment of the predictions made for the CASP6 protein structure prediction experiment conducted in 2004 in the New Fold category found the best models submitted bore an overall similarity to the target structure for three or four of the nine NF targets and for all but one of the FR/A targets. Expand
CASP6 assessment of contact prediction
TLDR
Comparisons of the predictions of the three best methods with those of CASP5/CAFASP3 suggested some improvement, although there were not enough targets in the comparisons to make this statistically significant. 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
Assessment of novel fold targets in CASP4: Predictions of three‐dimensional structures, secondary structures, and interresidue contacts
TLDR
In many cases, several groups were able to predict fragments of the target correctly—often at a level somewhat larger than standard supersecondary structures—but were not able to assemble fragments into a correct global topology. Expand
Successful ab initio prediction of the tertiary structure of NK‐lysin using multiple sequences and recognized supersecondary structural motifs
A simple approach to protein tertiary structure prediction is described, based on the assembly of recognized supersecondary structural fragments taken from highly resolved protein structures by usingExpand
LGA: a method for finding 3D similarities in protein structures
  • A. Zemla
  • Computer Science, Medicine
  • Nucleic Acids Res.
  • 2003
TLDR
Data generated by LGA can be successfully used in a scoring function to rank the level of similarity between two structures and to allow structure classification when many proteins are being analyzed. Expand
Prediction of local structure in proteins using a library of sequence-structure motifs.
TLDR
A new method for local protein structure prediction based on a library of short sequence pattern that correlate strongly with protein three-dimensional structural elements, and may contribute to ab initio tertiary structure prediction and fold recognition. Expand
CASP6 assessment of contact prediction. Proteins 2005;61(Suppl 7):214–224
  • 2005