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ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling
Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, The Institute of Technology. Swedish e-Science Research Center, Stockholm, Sweden.ORCID iD: 0000-0002-3772-8279
2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 15, 2221-2223 p.Article in journal (Refereed) Published
Abstract [en]

Model Quality Assessment Programs (MQAPs) are used to predict the quality of modeled protein structures. These usually use two approaches: methods using consensus of many alternative models and methods requiring only a single model to do its prediction. The consensus methods are useful to improve overall accuracy; however, they frequently fail to pick out the best possible model and cannot be used to generate and score new structures. Single-model methods, on the other hand, do not have these inherent shortcomings and can be used to both sample new structures and improve existing consensus methods. Here, we present ProQM-resample, a membrane protein-specific single-model MQAP, that couples side-chain resampling with MQAP rescoring by ProQM to improve model selection. The side-chain resampling is able to improve side-chain packing for 96% of all models, and improve model selection by 24% as measured by the sum of the Z-score for the first-ranked model (from 25.0 to 31.1), even better than the state-of-the-art consensus method Pcons. The improved model selection can be attributed to the improved side-chain quality, which enables the MQAP to rescue good backbone models with poor side-chain packing.

Place, publisher, year, edition, pages
Oxford University Press, 2014. Vol. 30, no 15, 2221-2223 p.
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:liu:diva-110276DOI: 10.1093/bioinformatics/btu187ISI: 000340049100023PubMedID: 24713439OAI: oai:DiVA.org:liu-110276DiVA: diva2:744049
Note

Funding Agencies|Swedish Research Council [2012-5270]; Carl Tryggers Stiftelse [12:516]

Available from: 2014-09-05 Created: 2014-09-05 Last updated: 2017-12-05Bibliographically approved

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