Literature DB >> 14681416

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli.

Shan Sundararaj1, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, David S Wishart.   

Abstract

The CyberCell Database (CCDB: http://redpoll. pharmacy.ualberta.ca/CCDB) is a comprehensive, web-accessible database designed to support and coordinate international efforts in modeling an Escherichia coli cell on a computer. The CCDB brings together both observed and derived quantitative data from numerous independent sources covering many aspects of the genomic, proteomic and metabolomic character of E.coli (strain K12). The database is self-updating but also supports 'community' annotation, and provides an extensive array of viewing, querying and search options including a powerful, easy-to-use relational data extraction system.

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Mesh：

Year:  2004        PMID： 14681416      PMCID： PMC308842          DOI： 10.1093/nar/gkh108

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  6 in total

1.  EcoGene: a genome sequence database for Escherichia coli K-12.

Authors:  K E Rudd
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The EcoCyc Database.

Authors:  Peter D Karp; Monica Riley; Milton Saier; Ian T Paulsen; Julio Collado-Vides; Suzanne M Paley; Alida Pellegrini-Toole; César Bonavides; Socorro Gama-Castro
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  Cell biology. Alliance launched to model E. coli.

Authors:  Constance Holden
Journal:  Science       Date:  2002-08-30       Impact factor: 47.728

4.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors:  A Bairoch; R Apweiler
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

5.  GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support.

Authors:  M Rebhan; V Chalifa-Caspi; J Prilusky; D Lancet
Journal:  Bioinformatics       Date:  1998       Impact factor: 6.937

6.  MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.

Authors:  M H Serres; M Riley
Journal:  Microb Comp Genomics       Date:  2000
  6 in total
  78 in total

1.  Label-free protein quantitation using weighted spectral counting.

Authors:  Christine Vogel; Edward M Marcotte
Journal:  Methods Mol Biol       Date:  2012

2.  Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion.

Authors:  Tadashi Ando; Jeffrey Skolnick
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-11       Impact factor: 11.205

3.  FtsZ Polymers Tethered to the Membrane by ZipA Are Susceptible to Spatial Regulation by Min Waves.

Authors:  Ariadna Martos; Ana Raso; Mercedes Jiménez; Zdeněk Petrášek; Germán Rivas; Petra Schwille
Journal:  Biophys J       Date:  2015-05-05       Impact factor: 4.033

4.  A model for protein translation: polysome self-organization leads to maximum protein synthesis rates.

Authors:  Hermioni Zouridis; Vassily Hatzimanikatis
Journal:  Biophys J       Date:  2006-11-10       Impact factor: 4.033

5.  Effects of codon distributions and tRNA competition on protein translation.

Authors:  Hermioni Zouridis; Vassily Hatzimanikatis
Journal:  Biophys J       Date:  2008-03-21       Impact factor: 4.033

6.  Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm.

Authors:  Douglas Ridgway; Gordon Broderick; Ana Lopez-Campistrous; Melania Ru'aini; Philip Winter; Matthew Hamilton; Pierre Boulanger; Andriy Kovalenko; Michael J Ellison
Journal:  Biophys J       Date:  2008-01-30       Impact factor: 4.033

7.  Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution.

Authors:  Dafyd J Jenkins; Dov J Stekel
Journal:  J Mol Evol       Date:  2010-02-12       Impact factor: 2.395

Review 8.  Beyond iron: non-classical biological functions of bacterial siderophores.

Authors:  Timothy C Johnstone; Elizabeth M Nolan
Journal:  Dalton Trans       Date:  2015-04-14       Impact factor: 4.390

9.  A protocol for generating a high-quality genome-scale metabolic reconstruction.

Authors:  Ines Thiele; Bernhard Ø Palsson
Journal:  Nat Protoc       Date:  2010-01-07       Impact factor: 13.491

Review 10.  Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome.

Authors:  Juan Javier Díaz-Mejía; Mohan Babu; Andrew Emili
Journal:  FEMS Microbiol Rev       Date:  2008-11-27       Impact factor: 16.408
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