TMFunction: Database for functional residues in membrane proteins

Nucleic Acids Research

Volumn 37, Issue SUPPL. 1, 2009, Pages

  Gromiha, M Michael ^a   Yabuki, Yukimitsu ^a   Suresh, M Xavier ^a   Thangakani, A Mary ^b   Suwa, Makiko ^a   Fukui, Kazuhiko ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b Advanced Technology Institute Inc   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; DISSOCIATION CONSTANT; FACTUAL DATABASE; IC 50; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT; STRUCTURE ACTIVITY RELATION; TMFUNCTION DATABASE; WILD TYPE;

AMINO ACIDS; DATABASES, PROTEIN; INTERNET; MEMBRANE PROTEINS; MUTATION;

EID: 58149177176     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn672     Document Type: Article

References (18)

1. Tusnady,G.E., Dosztanyi,Z. and Simon,I. (2005) PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 33, D275-D278.
2. Tusnady,G.E., Dosztanyi,Z. and Simon,I. (2005) TMDET: Web server for detecting transmembrane regions of proteins by using their 3D coordinates. Bioinformatics, 21, 1276-1277.
3. Saier,M.H. Jr, Tran,C.V. and Barabote,R.D. (2006) TCDB: The transporter classification database for membrane transport protein analyses and information. Nucleic Acids Res., 34, D181-D186.
4. Horn,F., Bettler,E., Oliveira,L., Campagne,F., Cohen,F.E. and Vriend,G. (2003) GPCRDB information system for G proteincoupled receptors. Nucleic Acids Res., 31, 294-297.
5. Schwacke,R., Schneider,A., Van Der Graaff,E., Fischer,K., Catoni,E., Desimone,M., Frommer,W.B., Flugge,U.I. and Kunze,R. (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol., 131, 16-26.
6. Edvardsen,O., Reiersen,A.L., Beukers,M.W. and Kristiansen,K. (2002) tGRAP, the G-protein coupled receptors mutant database. Nucleic Acids Res., 30, 361-363.
7. Kawabata,T., Ota,M. and Nishikawa,K. (1999) The Protein Mutant Database. Nucleic Acids Res., 27, 355-357.
8. Gromiha,M.M., An,J., Kono,H., Oobatake,M., Uedaira,H. and Sarai,A. (1999) ProTherm: Thermodynamic database for proteins and mutants. Nucleic Acids Res., 27, 286-288.
9. Hirokawa,T., Boon-Chieng,S. and Mitaku,S. (1998) SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics, 14, 378-379.
10. Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 305, 567-580.
11. Tusnády,G.E. and Simon,I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
12. Lehnert,U., Xia,Y., Royce,T.E., Goh,C.S., Liu,Y., Senes,A., Yu,H., Zhang,Z.L., Engelman,D.M. and Gerstein,M. (2004) Computational analysis of membrane proteins: Genomic occurrence, structure prediction and helix interactions. Q. Rev. Biophys., 37, 121-146.
13. Gromiha,M.M. and Suwa,M. (2007) Current developments on beta-barrel membrane proteins: Sequence and structure analysis, discrimination and prediction. Curr. Protein Pept. Sci., 8, 580-599.
14. Gromiha,M.M., Yabuki,Y., Kundu,S., Suharnan,S. and Suwa,M. (2007) TMBETA-GENOME: Database for annotated beta-barrel membrane proteins in genomic sequences. Nucleic Acids Res., 35, D314-D316.
15. Gromiha,M.M. and Yabuki,Y. (2008) Functional discrimination of membrane proteins using machine learning techniques. BMC Bioinform., 9 135.
16. Li,H., Dai,X. and Zhao,X. (2008) A nearest neighbor approach for automated transporter prediction and categorization from protein sequences. Bioinformatics, 24, 1129-1136.
17. Wu,C.H., Apweiler,R., Bairoch,A., Natale,D.A., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R. et al. (2006) The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res., 34, D187-D191.
18. Berman,H., Henrick,K., Nakamura,H. and Markley,J.L. (2007) The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.