NDLI: Protein Motif Retrieval by Secondary Structure Element Geometry and Biological Features Saliency

Content Provider	IEEE Xplore Digital Library
Author	Cantoni, V. Ferretti, M. Pellicano, N. Vandoni, J. Musci, M. Nugrahaningsih, N.
Copyright Year	2014
Description	Author affiliation: Dept. of Electr., Comput. & Biomed. Eng., Univ. of Pavia, Pavia, Italy (Cantoni, V.; Ferretti, M.; Pellicano, N.; Vandoni, J.; Musci, M.; Nugrahaningsih, N.)
Abstract	This paper presents an approach to detect the presence of a given motif in proteins or in protein data bank (PDB). The approach is based on the secondary structure elements (SSEs) geometrical arrangement in 3D space. A motif is represented as a set of SSEs in their specific positions related to a local reference system (LRS). We propose, exploiting the SSE biological feature saliency in the motif LRS construction stage, a planning strategy to speed-up the motif retrieval process. The experimentation has been carried out on a set of 20 proteins selected from the PDB. In detail we tested five different cases: (i) performances on searching a motif within single proteins, (ii) searching motifs on a set of proteins belonging to the same biological family, (iii) searching into single symmetric proteins, (iv) searching on a set of symmetric proteins from the same family, and finally (v) a general motif retrieval from the entire protein dataset. The experimental results showed good motif recognition performances on each test category, and, by exploiting the basic biological features saliency in motif construction, comparing to a previous approach of SSEs block geometrical retrieval based on the Generalized Hough Transform, it was revealed a significant decrease of the time/space computational complexity. It is worth to point out that the computation time for the case of motif absence is significantly lower than the case of motif present.
Starting Page	23
Ending Page	27
File Size	475667
Page Count	5
File Format	PDF
ISBN	9781479957217
ISSN	15294188
e-ISBN	9781479957224
DOI	10.1109/DEXA.2014.22
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2014-09-01
Publisher Place	Germany
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Protein engineering Vectors Geometry Computers pattern recognition protein motif retrieval secondary structure geometry feature
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
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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