Applying undertaker cost functions to model quality assessment

Archie, John G.; Karplus, Kevin

doi:10.1002/prot.22288

Cited by 18 publications

(21 citation statements)

References 23 publications

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“…The two servers that do not use consensus information come from the SAM‐T08‐MQA series. All of the SAM‐T08‐MQA servers51 use predicted contacts to assess the quality of the models52, 53 and the SAM‐T08‐MQAO server uses the predicted contacts alone. In addition, SMEG‐CCP appears to use contacts predicted from models to make their quality assessment predictions.…”

Section: Resultsmentioning

confidence: 99%

Predicted residue–residue contacts can help the scoring of 3D models

Tress

Valencia

2010

Proteins

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During the 7th Critical Assessment of Protein Structure Prediction (CASP7) experiment, it was suggested that the real value of predicted residue-residue contacts might lie in the scoring of 3D model structures. Here, we have carried out a detailed reassessment of the contact predictions made during the recent CASP8 experiment to determine whether predicted contacts might aid in the selection of close-to-native structures or be a useful tool for scoring 3D structural models. We used the contacts predicted by the CASP8 residue-residue contact prediction groups to select models for each target domain submitted to the experiment. We found that the information contained in the predicted residue-residue contacts would probably have helped in the selection of 3D models in the free modeling regime and over the harder comparative modeling targets. Indeed, in many cases, the models selected using just the predicted contacts had better GDT-TS scores than all but the best 3D prediction groups. Despite the well-known low accuracy of residue-residue contact predictions, it is clear that the predictive power of contacts can be useful in 3D model prediction strategies.

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Section: Resultsmentioning

confidence: 99%

Predicted residue–residue contacts can help the scoring of 3D models

Tress

Valencia

2010

Proteins

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“…Second, the consensus structural information from multiple templates is in general more accurate than that from the individual templates; this information can be exploited to correct the errors in the aligned regions of the template as well [37]. There are also a number of multiple-template based MQAP approaches, which try to score and rank models from a pool of multiple structures generated from other modeling algorithms [29,30•,38–40]. MQAP is usually able to produce a set of selected models having, on average, a better quality than the models from the individual algorithms; but the individual models are not refined by MQAP.…”

Section: Protein Structural Refinement: From Low To High Resolutionmentioning

confidence: 99%

Protein structure prediction: when is it useful?

Zhang

2009

Current Opinion in Structural Biology

245

192

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SummaryComputationally predicted three-dimensional structure of protein molecules has demonstrated the usefulness in many areas of biomedicine, ranging from approximate family assignments to precise drug screening. For nearly 40 years, however, the accuracy of the predicted models has been dictated by the availability of close structural templates. Progress has recently been achieved in refining lowresolution models closer to the native ones; this has been made possible by combining knowledgebased information from multiple sources of structural templates as well as by improving the energy funnel of physics-based force fields. Unfortunately, there has been no essential progress in the development of techniques for detecting remotely homologous templates and for predicting novel protein structures.

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“…The constraints have also been used for model quality assessment in evaluating models from other servers (22,13), but that application is not provided by the web server.…”

Section: Contact Predictionmentioning

confidence: 99%

SAM-T08, HMM-based protein structure prediction

Karplus

2009

Nucleic Acids Research

121

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The SAM-T08 web server is a protein structure prediction server that provides several useful intermediate results in addition to the final predicted 3D structure: three multiple sequence alignments of putative homologs using different iterated search procedures, prediction of local structure features including various backbone and burial properties, calibrated E-values for the significance of template searches of PDB and residue–residue contact predictions. The server has been validated as part of the CASP8 assessment of structure prediction as having good performance across all classes of predictions. The SAM-T08 server is available at http://compbio.soe.ucsc.edu/SAM_T08/T08-query.html

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Applying undertaker cost functions to model quality assessment

Cited by 18 publications

References 23 publications

Predicted residue–residue contacts can help the scoring of 3D models

Predicted residue–residue contacts can help the scoring of 3D models

Protein structure prediction: when is it useful?

SAM-T08, HMM-based protein structure prediction

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