Assessment of CASP7 structure predictions for template free targets

  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},
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
Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods
Assessment of CASP12 modeling efforts for targets with no obvious templates of high sequence/structure similarity in the PDB finds that despite this CASP being among the most challenging ones, a measurable improvement of the top predictions is apparent. Expand
Assessment of template‐based modeling of protein structure in CASP11
The results argue for a density‐driven approach in future CASP TBM assessments that accounts for the bimodal nature of these distributions instead of Z scores, which assume a unimodal, Gaussian distribution. Expand
Assessment of CASP7 predictions for template‐based modeling targets
The accuracy of predicted protein models for 108 target domains was assessed based on a detailed comparison between the experimental and predicted structures and it showed that the best groups produced models closer to the target structure than the best single template for a significant number of targets. Expand
Assessment of CASP8 structure predictions for template free targets
For template free model prediction, as evaluated in this CASP, successes have been achieved for most targets; however, a great deal of research is still required, both in improving the existing methods and in development of new approaches. Expand
An automatic method for CASP9 free modeling structure prediction assessment
Inspired by the experience in CASP9 FM category assessment, an automatic superimposition independent method named Quality Control Score (QCS) for structure prediction assessment is developed, which captures both global and local structural features, with emphasis on global topology. Expand
Domain definition and target classification for CASP7
Experimentally determined protein structures formed the basis of the CASP7 prediction assessments and were assigned to one or more tertiary structure prediction categories and where necessary were divided into structural domains. Expand
Assessment of template‐free modeling in CASP10 and ROLL
We present the assessment of predictions for Template‐Free Modeling in CASP10 and a report on the first ROLL experiment wherein predictions are collected year round for review at the regular CASPExpand
Assessment of CASP11 contact‐assisted predictions
An overview of contact‐assisted predictions in the eleventh round of critical assessment of protein structure prediction (CASP11), which included four categories: predicted contacts, correct contacts, simulated sparse NMR contacts, and cross‐linking contacts, highlighted a relatively poor overall performance. Expand
A multilayer evaluation approach for protein structure prediction and model quality assessment
A set of new QA methods were developed, including twoQA methods for evaluating target/template alignments, a molecular dynamics‐based QA method, and three consensus QA Methods with selected references to reveal new facets of protein structures complementary to the existing methods to guide the model generation and model selection in prediction. Expand
Assessment of the model refinement category in CASP12
The assessment of the model refinement predictions submitted to the 12th Experiment on the Critical Assessment of Protein Structure Prediction (CASP12) found eight groups that improve both the backbone conformation and the side chain positioning for the majority of targets. Expand


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CASP6 assessment of contact prediction
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
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
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
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.
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