Development of scoring functions for model quality estimation for membrane proteins
Project funded by own resources
Project title Development of scoring functions for model quality estimation for membrane proteins
Principal Investigator(s) Schwede, Torsten
Project Members Biasini, Marco
Studer, Gabriel
Organisation / Research unit Departement Biozentrum / Bioinformatics (Schwede)
Project Website http://swissmodel.expasy.org/qmean/
Project start 01.01.2011
Probable end 31.12.2016
Status Completed
Abstract

Quality assessment of protein structures is an important part of experimental structure validation and plays a crucial role in protein structure prediction. Most current scoring functions are primarily de-signed to rank alternative models of the same sequence supporting model selection whereas the prediction of the absolute quality of an individual protein model has received little attention in the field. However, reliable absolute quality estimates are crucial to assess the suitability of a model for specific biomedical applications. We have developed a new absolute measure for the quality of protein models, which provides an estimate of the “degree of nativeness” of the structural features observed in a model and describes the likelihood that a given model is of comparable quality to experimental structures. Model quality scores for individual models are expressed as “Z-scores” in comparison to scores obtained for high-resolution crystal structures. We demonstrated the ability of the newly introduced QMEAN Z-score to detect experimentally solved protein structures containing significant errors, as well as to evaluate theoretical protein models.

The second part of the project aims at the development of potentials of mean force tailered for membrane protein models.

Financed by Other funds

Published results ()

  ID Autor(en) Titel ISSN / ISBN Erschienen in Art der Publikation
156351  Benkert, P.; Tosatto, S.C.; Schwede, T.  Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust  1097-0134  Proteins  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156353  Benkert, P.; Kunzli, M.; Schwede, T.  QMEAN server for protein model quality estimation  1362-4962  Nucleic Acids Research  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156355  Benkert, P.; Schwede, T.; Tosatto, S.C.  QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information  1472-6807  BMC Structural Biology  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
156370  Thorsteinsdottir, H.B.; Schwede, T.; Zoete, V.; Meuwly, M.  How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding  1097-0134  Proteins  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
749244  Benkert, P.; Biasini, M.; Schwede, T.  Toward the estimation of the absolute quality of individual protein structure models    Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
1141161  Barbato, Alessandro; Benkert, Pascal; Schwede, Torsten; Tramontano, Anna; Kosinski, Jan  Improving your target-template alignment with MODalign.  1367-4811  Bioinformatics (Oxford, England)  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2158295  Mariani, Valerio; Biasini, Marco; Barbato, Alessandro; Schwede, Torsten  lDDT: A local superposition-free score for comparing protein structures and models using distance difference tests.  1367-4811  Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2158297  Kryshtafovych, Andriy; Barbato, Alessandro; Fidelis, Krzysztof; Monastyrskyy, Bohdan; Schwede, Torsten; Tramontano, Anna  Assessment of the assessment: Evaluation of the model quality estimates in CASP10.  1097-0134  Proteins  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 
2689815  Studer, Gabriel; Biasini, Marco; Schwede, Torsten  Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)  1367-4803  Bioinformatics  Publication: JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift) 

Cooperations ()

  ID Kreditinhaber Kooperationspartner Institution Laufzeit - von Laufzeit - bis
1533620  Schwede, Torsten  Tramontano, Anna  University of Rome  01.01.2009  31.12.2015 
2355647  Schwede, Torsten  Kryshtafovych, Andriy   UC Davis Genome Center  01.01.2009  31.12.2015 
   

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