Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/96903
Title: Cube-DB : detection of functional divergence in human protein families
Authors: Zhang, Zong Hong.
Bharatham, Kavitha.
Chee, Sharon M. Q.
Mihalek, Ivana.
Keywords: DRNTU::Science::Biological sciences
Issue Date: 2011
Source: Zhang, Z. H., Bharatham, K., Chee, S. M. Q., & Mihalek, I. (2011). Cube-DB: detection of functional divergence in human protein families. Nucleic Acids Research, 40(D1), D490-D494.
Series/Report no.: Nucleic acids research
Abstract: Cube-DB is a database of pre-evaluated results for detection of functional divergence in human/vertebrate protein families. The analysis is organized around the nomenclature associated with the human proteins, but based on all currently available vertebrate genomes. Using full genomes enables us, through a mutual-best-hit strategy, to construct comparable taxonomical samples for all paralogues under consideration. Functional specialization is scored on the residue level according to two models of behavior after divergence: heterotachy and homotachy. In the first case, the positions on the protein sequence are scored highly if they are conserved in the reference group of orthologs, and overlap poorly with the residue type choice in the paralogs groups (such positions will also be termed functional determinants). The second model additionally requires conservation within each group of paralogs (functional discriminants). The scoring functions are phylogeny independent, but sensitive to the residue type similarity. The results are presented as a table of per-residue scores, and mapped onto related structure (when available) via browser-embedded visualization tool. They can also be downloaded as a spreadsheet table, and sessions for two additional molecular visualization tools. The database interface is available at http://epsf.bmad.bii.a-star.edu.sg/cube/db/html/home.html.
URI: https://hdl.handle.net/10356/96903
http://hdl.handle.net/10220/10012
DOI: 10.1093/nar/gkr1129
Schools: School of Biological Sciences 
Rights: © 2011 The Author(s). This paper was published in Nucleic Acids Research and is made available as an electronic reprint (preprint) with permission of The Author(s). The paper can be found at the following official DOI: [http://dx.doi.org/10.1093/nar/gkr1129]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SBS Journal Articles

Files in This Item:
File Description SizeFormat 
13. Cube-DB detection of functional divergence.pdf547.92 kBAdobe PDFThumbnail
View/Open

SCOPUSTM   
Citations 50

3
Updated on Mar 18, 2024

Web of ScienceTM
Citations 50

3
Updated on Oct 28, 2023

Page view(s) 20

619
Updated on Mar 18, 2024

Download(s) 20

294
Updated on Mar 18, 2024

Google ScholarTM

Check

Altmetric


Plumx

Items in DR-NTU are protected by copyright, with all rights reserved, unless otherwise indicated.