NDLI: Meta-analysis of protein structural alignment

Content Provider	IEEE Xplore Digital Library
Author	Havrilla, J. Sacan, A.
Copyright Year	2012
Description	Author affiliation: School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America (Havrilla, J.; Sacan, A.)
Abstract	The three-dimensional structure of a protein molecule provides significant insight into its biological function. Structural alignment of proteins is an important and widely performed task in the analysis of protein structures, whereby functionally and evolutionarily important segments are identified. However, structural alignment is a computationally difficult problem and a large number of heuristics introduced to solve it do not agree on their results. Consequently, there is no widely accepted solution to the structure alignment problem. In this study, we present a meta-analysis approach to generate a re-optimized, best-of-all result using the alignments generated from several popular methods. Evaluations of the methods on a large set of benchmark pairwise alignments indicate that TM-align provides superior alignments (except for RMSD), compared to other methods we have surveyed. Smolign provides smaller cores than other methods with best RMSD values. The re-optimization of the alignments using TM-align's optimization method does not alter the relative performance of the methods. Additionally, visualization approaches to delineate the relationships of the alignment methods have been performed and their results provided.
Starting Page	72
Ending Page	76
File Size	1468134
Page Count	5
File Format	PDF
ISBN	9781467327466
e-ISBN	9781467327473
e-ISBN	9781467327442
DOI	10.1109/BIBMW.2012.6470218
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Protein engineering structure comparison benchmark test Clustering algorithms meta-analysis Software meta-program Synthetic aperture sonar Optimization Principal component analysis protein alignment
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
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