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URL: http://www.wholecellkb.org/
Proper Citation: WholeCellKB (RRID:SCR_004104)
Description: A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database.
Abbreviations: WholeCellKB
Synonyms: Mycoplasma genitalium database, WholeCellKB-MG, Whole Cell KB
Resource Type: web service, source code, database, data or information resource, data access protocol, model, software resource
Defining Citation: PMID:23175606, PMID:22817898
Keywords: model organism, whole-cell model, gene, protein, reaction, pathway, phenotype, genotype, simulation, cell, organism
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