title: TiD: Standalone software for mining putative drug targets from bacterial proteome.
abstract: TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application. Drug targets identified by TiD for Listeria monocytogenes, Bacillus anthracis and Pseudomonas aeruginosa have revealed significant overlaps with previous studies. TiD takes <2h to scan putative targets from a bacterial proteome with ~5000 proteins; hence, we propose it as a useful tool for rational drug design. TiD is available at http://bmicnip.in/TiD/.
authors.affiliation: University School of Information & Communication Technology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India. Electronic address: reena@ipu.ac.in.
authors.forename: Reena
authors.initials: R
authors.lastname: Gupta
authors.affiliation: Biomedical Informatics Centre, National Institute of Pathology-Indian Council of Medical Research, New Delhi 110029, India.
authors.forename: Dibyabhaba
authors.initials: D
authors.lastname: Pradhan
authors.affiliation: Biomedical Informatics Centre, National Institute of Pathology-Indian Council of Medical Research, New Delhi 110029, India.
authors.forename: Arun Kumar
authors.initials: AK
authors.lastname: Jain
authors.affiliation: University School of Information & Communication Technology, Guru Gobind Singh Indraprastha University, New Delhi 110078, India. Electronic address: csrai@ipu.ac.in.
authors.forename: Chandra Shekhar
authors.initials: CS
authors.lastname: Rai
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology / Q000627:therapeutic use*; D001419:Bacteria / Q000187:drug effects* / Q000378:metabolism; D001426:Bacterial Proteins / Q000187:drug effects*; D055808:Drug Discovery / Q000379:methods*; D023281:Genomics / Q000379:methods; D058990:Molecular Targeted Therapy; D020543:Proteome / Q000187:drug effects; D012984:Software
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D020543:Proteome
keywords: Automated target identification; Essential genes; Subtractive genomic analysis; TiD