title: A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks.
abstract: The genetic, proteomic, disease and pharmacological studies have generated rich data in protein interaction, disease regulation and drug activities useful for systems-level study of the biological, disease and drug therapeutic processes. These studies are facilitated by the established and the emerging computational methods. More recently, the network descriptors developed in other disciplines have become more increasingly used for studying the protein-protein, gene regulation, metabolic, disease networks. There is an inadequate coverage of these useful network features in the public web servers. We therefore introduced upto 313 literature-reported network descriptors in PROFEAT web server, for describing the topological, connectivity and complexity characteristics of undirected unweighted (uniform binding constants and molecular levels), undirected edge-weighted (varying binding constants), undirected node-weighted (varying molecular levels), undirected edge-node-weighted (varying binding constants and molecular levels) and directed unweighted (oriented process) networks. The usefulness of the PROFEAT computed network descriptors is illustrated by their literature-reported applications in studying the protein-protein, gene regulatory, gene co-expression, protein-drug and metabolic networks. PROFEAT is accessible free of charge at http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhang
authors.forename: Lin
authors.initials: L
authors.lastname: Tao
authors.forename: Xian
authors.initials: X
authors.lastname: Zeng
authors.forename: Chu
authors.initials: C
authors.lastname: Qin
authors.forename: Shangying
authors.initials: S
authors.lastname: Chen
authors.forename: Feng
authors.initials: F
authors.lastname: Zhu
authors.forename: Zerong
authors.initials: Z
authors.lastname: Li
authors.forename: Yuyang
authors.initials: Y
authors.lastname: Jiang
authors.forename: Weiping
authors.initials: W
authors.lastname: Chen
authors.forename: Yu-Zong
authors.initials: YZ
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004194:Disease / Q000145:classification*; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D053858:Metabolic Networks and Pathways; D004364:Pharmaceutical Preparations; D025941:Protein Interaction Mapping; D012984:Software; D049490:Systems Biology / Q000379:methods
chemical_list: D004364:Pharmaceutical Preparations
keywords: biological network; network descriptor; network feature; web server