Searching Protein 3-D Structures for Optimal Structure Alignment Using Intelligent Algorithms and Data Structures

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989100%3A27240%2F10%3A86075394" target="_blank" >RIV/61989100:27240/10:86075394 - isvavai.cz</a>
Result on the web
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DOI - Digital Object Identifier
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Result language
angličtina
Original language name
Searching Protein 3-D Structures for Optimal Structure Alignment Using Intelligent Algorithms and Data Structures
Original language description
In this paper, we present a novel algorithm for measuring protein similarity based on their 3-D structure (protein tertiary structure). The algorithm used a suffix tree for discovering common parts of main chains of all proteins appearing in the currentresearch collaboratory for structural bioinformatics protein data bank (PDB). By identifying these common parts, we build a vector model and use some classical information retrieval (IR) algorithms based on the vector model to measure the similarity between proteins-all to all protein similarity. For the calculation of protein similarity, we use term frequency x inverse document frequency (tf x idf) term weighing schema and cosine similarity measure. The goal of this paper is to introduce new protein similarity metric based on suffix trees and IR methods. Whole current PDB database was used to demonstrate very good time complexity of the algorithm as well as high precision.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
IN - Informatics
OECD FORD branch
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Publication year
2010
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical
IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE
ISSN
1089-7771
e-ISSN
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Volume of the periodical
14
Issue of the periodical within the volume
6
Country of publishing house
US - UNITED STATES
Number of pages
9
Pages from-to
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UT code for WoS article
000283982200008
EID of the result in the Scopus database
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