NDLI: Using structural domains to predict obligate and non-obligate protein-protein interactions

Content Provider	IEEE Xplore Digital Library
Author	Maleki, M. Hall, M. Rueda, L.
Copyright Year	2012
Description	Author affiliation: School of Computer Science, University of Windsor, 401 Sunset Ave., ON, N9B3P4, Canada (Maleki, M.; Hall, M.; Rueda, L.)
Abstract	The identification and prediction of particular types of protein-protein interactions (PPIs) based on knowledge of their interacting domains is a problem that has drawn the attention of researchers in the past few years. We focus on the prediction and analysis of obligate and non-obligate complexes by using structural domains from the CATH database. Our proposed prediction model uses desolvation energies of domain-domain interactions (DDIs) present in the interfaces of such complexes. The prediction is performed via linear dimensionality reduction (LDR) and support vector machines (SVMs). Our results on two well-known datasets show that DDI features of the first three levels of CATH, especially level 2, are more powerful and discriminative than features of other levels in predicting these types of complexes. Furthermore, a detailed analysis shows that different DDIs are present in obligate and non-obligate complexes, and that homo-DDIs are more likely to be present in obligate interactions.
Starting Page	9
Ending Page	15
File Size	1230582
Page Count	7
File Format	PDF
ISBN	9781467311908
e-ISBN	9781467311915
DOI	10.1109/CIBCB.2012.6217204
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-05-09
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Support vector machines Proteins Amino acids Accuracy Vectors Kernel Transient analysis complex type prediction protein-protein interaction domain-domain interaction CATH
Content Type	Text
Resource Type	Article

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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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