NDLI: A novel method for protein 3D-structure similarity measure based on n-gram modeling

Content Provider	IEEE Xplore Digital Library
Author	Razmara, J. Deris, S.B.
Copyright Year	2008
Description	Author affiliation: Fac. of Comput. Sci. & Inf. Syst., Univ. Teknol. Malaysia, Skudai (Razmara, J.; Deris, S.B.)
Abstract	The present paper describes a novel method for measuring structural similarity of proteins in three dimensions. The method gets its roots from computational linguistics and the related techniques for modeling protein structure in string form and pairwise comparison of protein sequences. The method uses n-gram based modeling techniques for capturing regularities in protein structure sequences and joints cross-entropy measures for comparing two protein sequences to do similarity test. In this way, the 3D structure of protein is represented in string form and, then, a similarity test is performed over these sequences. To find an overlap between two protein structures in 3D-space, a superposition task is also applied. In order to confirm the validity of this method, some experiments were performed using a collection of the protein data sets on publicly available servers which showed that the method is efficient.
Starting Page	1
Ending Page	6
File Size	347882
Page Count	6
File Format	PDF
ISBN	9781424428441
DOI	10.1109/BIBE.2008.4696719
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-10-08
Publisher Place	Greece
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Biological system modeling Computational linguistics Testing Bioinformatics Amino acids Dynamic programming Computer science Management information systems Algorithm design and analysis
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
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
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Text-Based Protein Structure Modeling for Structure Comparison

A novel efficient protein similarity measure based on n-gram modeling (2005)

Fast Dynamic Programming Based Sequence Alignment Algorithm

Evolving Models of Biological Sequence Similarity

On Predicting Protein Secondary Structure from their Aminoacid Sequences using Inductive Logic Programming

3D protein model assessment using geometric and biological features

DALIX: Optimal DALI Protein Structure Alignment

DALIX: Optimal DALI Protein Structure Alignment

How to Fold Amino Acid Interaction Networks by Computational Intelligence Methods

A novel method for protein 3D-structure similarity measure based on n-gram modeling

Similar Documents

Text-Based Protein Structure Modeling for Structure Comparison

A novel efficient protein similarity measure based on n-gram modeling (2005)

Fast Dynamic Programming Based Sequence Alignment Algorithm

Evolving Models of Biological Sequence Similarity

On Predicting Protein Secondary Structure from their Aminoacid Sequences using Inductive Logic Programming

3D protein model assessment using geometric and biological features

DALIX: Optimal DALI Protein Structure Alignment

DALIX: Optimal DALI Protein Structure Alignment

How to Fold Amino Acid Interaction Networks by Computational Intelligence Methods

A novel method for protein 3D-structure similarity measure based on n-gram modeling