Generation of efficient fingerprint for GFP-like fold and computational identification of potential GFP-like homologs

Edwardraja, Selvakumar, Munussami, Ganapathiraman, Goyal, Amit and Lee, Sun-Gu (2016) Generation of efficient fingerprint for GFP-like fold and computational identification of potential GFP-like homologs. Biotechnology and Bioprocess Engineering, 21 6: 712-719. doi:10.1007/s12257-016-0362-7


Author Edwardraja, Selvakumar
Munussami, Ganapathiraman
Goyal, Amit
Lee, Sun-Gu
Title Generation of efficient fingerprint for GFP-like fold and computational identification of potential GFP-like homologs
Journal name Biotechnology and Bioprocess Engineering   Check publisher's open access policy
ISSN 1976-3816
1226-8372
Publication date 2016-11-01
Year available 2017
Sub-type Article (original research)
DOI 10.1007/s12257-016-0362-7
Open Access Status Not yet assessed
Volume 21
Issue 6
Start page 712
End page 719
Total pages 8
Place of publication Seoul, Korea
Publisher Korean Society for Biotechnology and Bioengineering
Collection year 2017
Language eng
Formatted abstract
There is a considerable interest in the detection of GFP-like proteins due to their structural stability and functional usefulness. GFP-like proteins share highly conserved beta-barrel fold with 11 beta-strands. However, their low sequence identity hampers efficient identification of their homologous proteins from database. In this study, an attempt was made to generate a fingerprint for efficient detection of GFP-like proteins. Overlapped conserved residues (OCR)-based approach has been used to design a protein fingerprint based on sequentially and structurally conserved residues in secondary structures to detect homologous proteins very efficiently. Therefore, a fingerprint for GFP-like fold was designed using the OCR approach. However, its specificity was too low to be used for the identification of novel proteins. The conserved residues of loop regions were added and optimized to improve its specificity without losing its high sensitivity. The optimized fingerprint was employed to scan NR database. A total of 20 hypothetical proteins were detected, among which nine were validated as potential GFP-like homologs.
Keyword GFP-like fold
Homolog detection
OCR
Overlapped conserved residues
Protein fingerprint
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 0 times in Thomson Reuters Web of Science Article
Scopus Citation Count Cited 0 times in Scopus Article
Google Scholar Search Google Scholar
Created: Fri, 21 Apr 2017, 11:36:29 EST by Selvakumar Edwardraja on behalf of Learning and Research Services (UQ Library)