Note_Metabolites – Metabolites

Name
WID Note_Metabolites
Name Metabolites
 
Comments
Comments Metabolite structures were compiled from several sources including the databases BioCyc [PUB_0006], ChEBI [PUB_0593], Delta Mass [PUB_0589], FindMod [PUB_0590], KEGG [PUB_0113], LIPID MAPS [PUB_0588], Modomics [PUB_0267], PubChem [PUB_0587], RESID [PUB_0592], UniMod [PUB_0591] and the Feist et al E. coli FBA model [PUB_0558]. Metabolite hydrophobicity was predicted by ExPASy ProtParam [PUB_0585]. Metabolite traditional and IUPAC names, pI, logP, logD, van der Waals volume, and smiles were computed by ChemAxon Marvin [PUB_0594].
References
  1. . Marvin. (None). WholeCell: PUB_0594, URL: http://www.chemaxon.com/marvin/

  2. Creasy DM, Cottrell JS. Unimod: Protein modifications for mass spectrometry. Proteomics 4, 1534-6 (2004). WholeCell: PUB_0591, PubMed: 15174123, URL: http://www.unimod.org/

  3. Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 34, D145-9 (2006). WholeCell: PUB_0267, PubMed: 16381833, URL: http://modomics.genesilico.pl/

  4. Fahy E, Sud M, Cotter D, Subramaniam S. LIPID MAPS online tools for lipid research. Nucleic Acids Res 35, W606-12 (2007). WholeCell: PUB_0588, PubMed: 17584797, URL: http://www.lipidmaps.org/

  5. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3, 121 (2007). WholeCell: PUB_0558, PubMed: 17593909

  6. ... 6 more

  7. Garavelli JS. The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics 4, 1527-33 (2004). WholeCell: PUB_0592, PubMed: 15174122, URL: http://home.earthlink.net/~jsgaravelli/RESIDInfo.HTML

  8. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 36, D480-4 (2008). WholeCell: PUB_0113, PubMed: 18077471, URL: http://www.genome.jp/kegg/

  9. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  10. Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 37, W623-33 (2009). WholeCell: PUB_0587, PubMed: 19498078, URL: http://pubchem.ncbi.nlm.nih.gov/

  11. Wilkins MR, Gasteiger E, Bairoch A, Sanchez JC, Williams KL, Appel RD, Hochstrasser DF. Protein identification and analysis tools in the ExPASy server. Methods Mol Biol 112, 531-52 (1999). WholeCell: PUB_0585, PubMed: 10027275, URL: http://ca.expasy.org/tools/protparam.html

  12. de Matos P, Alcántara R, Dekker A, Ennis M, Hastings J, Haug K, Spiteri I, Turner S, Steinbeck C. Chemical Entities of Biological Interest: an update. Nucleic Acids Res 38, D249-54 (2010). WholeCell: PUB_0593, PubMed: 19854951, URL: http://www.ebi.ac.uk/chebi/

 
Metadata
Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:57