Annotation-based inference of transporter function

Bioinformatics

Volumn 24, Issue 13, 2008, Pages

  Lee, Thomas J ^a   Paulsen, Ian ^b   Karp, Peter ^a  

^a SRI INTERNATIONAL   (United States)

^b MACQUARIE UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN;

ACCURACY; ALGORITHM; ARTICLE; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN METABOLISM; PROTEIN TRANSPORT;

FORECASTING; GENES; INTELLIGENT SYSTEMS; METABOLISM; MOLECULAR BIOLOGY; QUERY LANGUAGES;

AUTOMATICALLY GENERATED; COMPARATIVE ANALYSIS; COMPUTATIONAL ANALYSIS; DECLARATIVE DESCRIPTIONS; PRECISION AND RECALL; REACTION PREDICTION; TRANSPORT CAPABILITIES; TRANSPORTER PROTEINS;

PROTEINS;

EID: 46249122830     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn180     Document Type: Article

References (19)

1. Bult,C.J. et al. (2008) The mouse genome database (MGD): Mouse biology and model systems. Nucleic Acids Res., 36, D724-D728.
2. Caspi,R. et al. (2006) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 34, D511-D516.
3. Caspi,R. et al. (2008) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 36, D623-D631.
4. Chisholm,R.L. et al. (2006) Dictybase, the model organism database for dictyostelium discoideum. Nucleic Acids Res., 34, D423-D427.
5. Consortium,G.O. (2008) The gene ontology project in 2008. Nucleic Acids Res., 36, D440-D444.
6. Feist,A. et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli k-12 mg1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3, Article121.
7. Karp,P. (2001) Pathway databases: A case study in computational symbolic theories. Science, 293, 2040-2044.
8. Karp,P. et al. (2002) The Pathway Tools Software. Bioinformatics, 18, S225-S232.
9. Karp,P. et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res., 33 6083-6089.
10. Keseler,I. et al. (2007) Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res., 35, 7577-7590.
11. Krummenacker,M. et al. (2005) Querying and computing with BioCyc databases. Bioinformatics, 21, 3454-3455.
12. Lin,H.H. et al. (2006) Prediction of transporter family from protein sequence by support vector machine approach. Proteins, 62, 218-231.
13. Mo,M.L. et al. (2007) A genome-scale, constraint-based approach to systems biology of human metabolism. Mol. Biosyst., 3, 598-603.
14. Nash,R. et al. (2007) Expanded protein information at sgd: New pages and proteome browser. Nucleic Acids Res., 35, D468-D471.
15. Paley,S. and Karp,P. (2006) The Pathway Tools cellular overview diagram and omics viewer. Nucleic Acids Res., 34, 3771-3778.
16. Ren,Q. et al. (2007) TransportDB: A comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. Nucleic Acids Res., 35, D274-D279.
17. Romero,P. and Karp,P. (2004) Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway/genome databases. Bioinformatics, 20, 709-717.
18. Rzhetsky,A. et al. (2004) GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Inform., 37, 43-53.
19. Saier,M.H. et al. (2006) TCDB: The transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res., 34, D181-D186.