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Sequence-based prediction and characterization of disorder-to-order transitioning binding sites in proteins Open Access


Other title
Disorder Prediction
Flexible binding sites
Disordered binding sites
Sequence based prediction
Protein Disorder
Molecular Recognition Features
MoRF prediction
Type of item
Degree grantor
University of Alberta
Author or creator
Miri Disfani, Fatemeh
Supervisor and department
Kurgan, Lukasz (Electrical and Computer Engineering)
Examining committee member and department
Tuszynski, Jack A.(Physics)
Reformat, Marek (Electrical and Computer Engineering)
Department of Electrical and Computer Engineering
Software Engineering and Intelligent Systems
Date accepted
Graduation date
Master of Science
Degree level
Molecular Recognition Feature (MoRF) regions are disordered binding sites that become structured upon binding. MoRFs are implicated in important biological processes, including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains. We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (, , coil, and complex). We develop a comprehensive dataset of annotated MoRFs and use it to build and empirically compare our method. Empirical evaluation shows that MoRFpred statistically significantly outperforms existing predictors by 0.07 in AUC and 10% in success rate. We show that our predicted MoRF regions have non-random sequence similarity with native MoRFs. We use this observation along with the fact that predictions with higher probability are more accurate to identify putative MoRF regions. We present case studies to analyze these putative MoRFs.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
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