NDLI: Predicting protein folding cores based on complex network and phylogenetic analyses

Content Provider	IEEE Xplore Digital Library
Author	Haiyan Li
Copyright Year	2009
Description	Author affiliation: Key Lab of Biophysics in Universities of Shandong, Dezhou university 253023, China (Haiyan Li)
Abstract	A crucial event of protein folding is the formation of a folding core, which is the subset of the protein's structure that is the first to form during folding and the last to break during denaturation. Both experimental and simulation techniques to capture folding core membership have found it challenging. In this paper, the six different computational prediction methods were proposed to predict folding core residues from a protein structure. The protein structure is modeled as an undirected network with the amino acids the vertexes and the contacts between them the edges. We find that the core residues have mainly high degree and low clustering coefficient compared with the surface residues. The closeness values of core residues are similar with the surface residues. The degree distribution of core and surface residues all are Poisson distribution. This suggests that the same small-world organization prevails throughout the protein, despite the heterogeneous density distribution. The six different centrality measurements have been proposed to predict folding core residues from a set of 14 well-characterized proteins. We show that the six measurements (degree, clustering coefficient, closeness centrality, betweenness, conservation score and solvent accessible surface area) all accurately detect the folding core residues. The best methods are based on the solvent accessible surface area and the local centrality measurement closeness. This indicates that the folding core residues have high hydrophobicity and tightness packed.
Starting Page	354
Ending Page	357
File Size	2065502
Page Count	4
File Format	PDF
ISBN	9781424446902
DOI	10.1109/FBIE.2009.5405844
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-12-13
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Solvents Protein engineering Computational modeling Area measurement Prediction methods Amino acids Educational institutions Phylogeny Biomedical measurements Protein structure networks Folding core Complex networks Network Phylogenetic analyses
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