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J Mol Biol. 2017 Feb 3;429(3):416-425. doi: 10.1016/j.jmb.2016.10.013. Epub 2016 Oct 12.

PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks.

Author information

1
Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore.
2
School of Medicine, Hangzhou Normal University, Hangzhou 310012, P.R. China.
3
Innovative Drug Research Centre and College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P.R. China.
4
State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, P.R. China.
5
College of Chemistry, Sichuan University, Chengdu 610064, P.R. China; Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, West China School of Medicine, Sichuan University, Chengdu 610041, P.R. China. Electronic address: lizerong@scu.edu.cn.
6
Key Lab of Agricultural Products Processing and Quality Control of Nanchang City, Jiangxi Agricultural University, Nanchang 330045, P.R. China. Electronic address: iaochen@163.com.
7
Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore. Electronic address: phacyz@nus.edu.sg.

Abstract

The studies of biological, disease, and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web servers for computing network descriptors, but many descriptors are not covered, including those used or useful for biological studies. We upgraded the PROFEAT web server http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi for computing up to 329 network descriptors and protein-protein interaction descriptors. PROFEAT network descriptors comprehensively describe the topological and connectivity characteristics of unweighted (uniform binding constants and molecular levels), edge-weighted (varying binding constants), node-weighted (varying molecular levels), edge-node-weighted (varying binding constants and molecular levels), and directed (oriented processes) networks. The usefulness of the network descriptors is illustrated by the literature-reported studies of the biological networks derived from the genome, interactome, transcriptome, metabolome, and diseasome profiles.

KEYWORDS:

Web server; biological network; biological pathway; network descriptor; protein descriptor

PMID:
27742592
DOI:
10.1016/j.jmb.2016.10.013
[Indexed for MEDLINE]

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