Literature DB >> 11752254

The MetaCyc Database.

Peter D Karp1, Monica Riley, Suzanne M Paley, Alida Pellegrini-Toole.   

Abstract

MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms. MetaCyc is a review-level database in that a given entry in MetaCyc often integrates information from multiple literature sources. The pathways in MetaCyc were determined experimentally, and are labeled with the species in which they are known to occur based on literature references examined to date. MetaCyc contains extensive commentary and literature citations. Applications of MetaCyc include pathway analysis of genomes, metabolic engineering and biochemistry education. MetaCyc is queried using the Pathway Tools graphical user interface, which provides a wide variety of query operations and visualization tools. MetaCyc is available via the World Wide Web at http://ecocyc.org/ecocyc/metacyc.html, and is available for local installation as a binary program for the PC and the Sun workstation, and as a set of flatfiles. Contact metacyc-info@ai.sri.com for information on obtaining a local copy of MetaCyc.

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Year:  2002        PMID: 11752254      PMCID: PMC99148          DOI: 10.1093/nar/30.1.59

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


  1 in total

1.  Integrated pathway-genome databases and their role in drug discovery.

Authors:  P D Karp; M Krummenacker; S Paley; J Wagg
Journal:  Trends Biotechnol       Date:  1999-07       Impact factor: 19.536

  1 in total
  110 in total

Review 1.  Network genomics--a novel approach for the analysis of biological systems in the post-genomic era.

Authors:  Christian V Forst
Journal:  Mol Biol Rep       Date:  2002-09       Impact factor: 2.316

2.  Enzyme-specific profiles for genome annotation: PRIAM.

Authors:  Clotilde Claudel-Renard; Claude Chevalet; Thomas Faraut; Daniel Kahn
Journal:  Nucleic Acids Res       Date:  2003-11-15       Impact factor: 16.971

3.  Protein complexes and functional modules in molecular networks.

Authors:  Victor Spirin; Leonid A Mirny
Journal:  Proc Natl Acad Sci U S A       Date:  2003-09-29       Impact factor: 11.205

4.  MetaCyc: a multiorganism database of metabolic pathways and enzymes.

Authors:  Cynthia J Krieger; Peifen Zhang; Lukas A Mueller; Alfred Wang; Suzanne Paley; Martha Arnaud; John Pick; Seung Y Rhee; Peter D Karp
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  A guide to building image-centric databases.

Authors:  William Bug; Jonathan Nissanov
Journal:  Neuroinformatics       Date:  2003

6.  Pathway length and evolutionary constraint in amino acid biosynthesis.

Authors:  Matthew T Rutter; Rebecca A Zufall
Journal:  J Mol Evol       Date:  2004-02       Impact factor: 2.395

7.  High-throughput generation, optimization and analysis of genome-scale metabolic models.

Authors:  Christopher S Henry; Matthew DeJongh; Aaron A Best; Paul M Frybarger; Ben Linsay; Rick L Stevens
Journal:  Nat Biotechnol       Date:  2010-08-29       Impact factor: 54.908

8.  Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms.

Authors:  Karen R Christie; Shuai Weng; Rama Balakrishnan; Maria C Costanzo; Kara Dolinski; Selina S Dwight; Stacia R Engel; Becket Feierbach; Dianna G Fisk; Jodi E Hirschman; Eurie L Hong; Laurie Issel-Tarver; Robert Nash; Anand Sethuraman; Barry Starr; Chandra L Theesfeld; Rey Andrada; Gail Binkley; Qing Dong; Christopher Lane; Mark Schroeder; David Botstein; J Michael Cherry
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

9.  Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches.

Authors:  Akriti Srivastava; Pallavi Somvanshi; Bhartendu Nath Mishra
Journal:  Syst Synth Biol       Date:  2012-12-30

10.  Molecular models of protein targets from Mycobacterium tuberculosis.

Authors:  Nelson José Freitas da Silveira; Hugo Brandão Uchôa; José Henrique Pereira; Fernanda Canduri; Luiz Augusto Basso; Mário Sérgio Palma; Diógenes Santiago Santos; Walter Filgueira de Azevedo
Journal:  J Mol Model       Date:  2005-03-10       Impact factor: 1.810

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