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ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling
KTH, Centres, SeRC - Swedish e-Science Research Centre. Linköping Univ, Dept Phys Chem & Biol, SE-58183 Linköping, Sweden..
2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 15, p. 2221-2223Article 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 UNIV PRESS , 2014. Vol. 30, no 15, p. 2221-2223
Keywords [en]
SECONDARY STRUCTURE, PREDICTION, FEATURES
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-269191DOI: 10.1093/bioinformatics/btu187ISI: 000340049100023PubMedID: 24713439Scopus ID: 2-s2.0-84905040919OAI: oai:DiVA.org:kth-269191DiVA, id: diva2:1412613
Note

QC 20200306

Available from: 2020-03-06 Created: 2020-03-06 Last updated: 2020-06-03Bibliographically approved

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