NDLI: Score matrix optimization for quartz binding peptides using evolutionary strategy

Content Provider	IEEE Xplore Digital Library
Author	Senliol, B. Cataltepe, Z.
Copyright Year	2009
Description	Author affiliation: Bilgisayar Mühendisli¿i Bölümü, ¿stanbul Teknik Üniversitesi, Türkiye (Senliol, B.; Cataltepe, Z.)
Abstract	Finding new peptides that can bind to some inorganic materials with high affinity and specificity is an active research problem with many application areas ranging from medicine to electronics. While it is easier to design peptides in-silico, in-vitro testing of binding is a slow and expensive process. Peptides with similar structure usually have similar functions. Score matrices, such as Blosum, PAM and Gonnet are used to score amino acid replacements in alignment algorithms such as Needleman-Wunsch or Smith-Waterman which measure similarity between two sequences. These score matrices may not represent the frequency of amino-acids replacement for experimental data. Score matrices which are optimized for specific peptide class or function have an important effect on accurate classification of artificial or newly discovered peptides. In this paper, score matrices that are specific to quartz binding peptides are derived using an evolutionary strategy (ES) and performance of these matrices are compared with the Quartz I matrix of Oren et.al. (2007). Results show that the matrices which obtained from the ES have better performance than Quartz I matrix when TSS (total similarity score) is used as a performance measurement criterion. Using ES scoring matrices and TSS for classifying peptides as strong, moderate or weak has performed 30% better in terms of accuracy and 40% better in terms of the number of inversions of affinity ordering of peptides than Quartz I matrix.
Starting Page	388
Ending Page	391
File Size	466284
Page Count	4
File Format	PDF
ISBN	9781424444359
DOI	10.1109/SIU.2009.5136414
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-04-09
Publisher Place	Turkey
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Measurement Sequences Peptides Inorganic materials Amino acids Frequency In vitro Testing
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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