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

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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 current research 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. 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 current research 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. (en)
Title	Searching Protein 3-D Structures for Optimal Structure Alignment Using Intelligent Algorithms and Data Structures Searching Protein 3-D Structures for Optimal Structure Alignment Using Intelligent Algorithms and Data Structures (en)
skos:prefLabel	Searching Protein 3-D Structures for Optimal Structure Alignment Using Intelligent Algorithms and Data Structures Searching Protein 3-D Structures for Optimal Structure Alignment Using Intelligent Algorithms and Data Structures (en)
skos:notation	RIV/61989100:27240/10:86075394!RIV11-MSM-27240___
http://linked.open...avai/riv/aktivita	S
http://linked.open...avai/riv/aktivity	S
http://linked.open...iv/cisloPeriodika	6
http://linked.open...vai/riv/dodaniDat	2011
http://linked.open...aciTvurceVysledku	Snášel, Václav Abraham Padath, Ajith
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Vysoká škola báňská - Technická univerzita Ostrava / Fakulta elektrotechniky a informatiky
http://linked.open...dnocenehoVysledku	286577
http://linked.open...ai/riv/idVysledku	RIV/61989100:27240/10:86075394
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	Structures; Data; and; Algorithms; Intelligent; Using; Alignment; Structure; Optimal; for; Structures; 3-D; Protein; Searching (en)
http://linked.open.../riv/klicoveSlovo	Alignment Intelligent for Protein Algorithms Structure Structures and Data Searching Using 3-D Optimal
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[385B2A8E12E7]
http://linked.open...i/riv/nazevZdroje	IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE
http://linked.open...in/vavai/riv/obor	IN
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...UplatneniVysledku	2010
http://linked.open...v/svazekPeriodika	14
http://linked.open...iv/tvurceVysledku	Abraham Padath, Ajith Snášel, Václav Novosád, Tomáš Yang, Jack Y.
http://linked.open...ain/vavai/riv/wos	000283982200008
issn	1089-7771
number of pages	9 (xsd:int)
http://localhost/t...ganizacniJednotka	27240

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