title: PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks.
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.
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore.
authors.forename: P
authors.initials: P
authors.lastname: Zhang
authors.affiliation: School of Medicine, Hangzhou Normal University, Hangzhou 310012, P.R. China.
authors.forename: L
authors.initials: L
authors.lastname: Tao
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore.
authors.forename: X
authors.initials: X
authors.lastname: Zeng
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore.
authors.forename: C
authors.initials: C
authors.lastname: Qin
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore.
authors.forename: S Y
authors.initials: SY
authors.lastname: Chen
authors.affiliation: Innovative Drug Research Centre and College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P.R. China.
authors.forename: F
authors.initials: F
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, P.R. China.
authors.forename: S Y
authors.initials: SY
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Z R
authors.initials: ZR
authors.lastname: Li
authors.affiliation: 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.
authors.forename: W P
authors.initials: WP
authors.lastname: Chen
authors.affiliation: Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore. Electronic address: phacyz@nus.edu.sg.
authors.forename: Y Z
authors.initials: YZ
authors.lastname: Chen
mesh_terms: D019295:Computational Biology; D053263:Gene Regulatory Networks; D015894:Genome, Human; D006801:Humans; D020407:Internet; D055442:Metabolome; D008962:Models, Theoretical; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D012984:Software; D059467:Transcriptome
chemical_list: D011506:Proteins
keywords: Web server; biological network; biological pathway; network descriptor; protein descriptor