PoreLogo: A new tool to analyse, visualize and compare channels in transmembrane proteins

Bioinformatics

Volumn 25, Issue 23, 2009, Pages 3183-3184

  Oliva, Romina ^a,b   Thornton, Janet M ^b   Pellegrini Calace, Marialuisa ^b  

^a UNIVERSITY OF NAPLES PARTHENOPE   (Italy)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 75949128474     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp545     Document Type: Article

References (12)

1. Altschul, S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Apweiler, R. et al. (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res., 32, D115-D119.
3. Crooks, G.E. et al. (2004) Weblogo: a sequence logo generator. Genome Res., 14, 1188-1190.
4. Doerr, A. (2009) Membrane protein structures. Nat. Methods, 6, 35.
5. Gonen, T. and Walz, T. (2006) The structure of aquaporins. Q. Rev. Biophys., 39, 361-396.
6. Pellegrini-Calace, M.L. et al. (2009) Pore-Walker: a novel tool for the identification and characterization of channels in transmembrane proteins from their three dimensional structure. PLOS Comput. Biol., 5, E1000440.
7. Ramsey, I.S. et al. (2006) An introduction to TRP channels. Annu. Rev. Physiol., 68, 619-647.
8. Shealy, R.T. et al. (2003) Sequence-function analysis of the K+ selective family of ion channels using a comprehensive alignment and the Kcsa channel structure. Biophys. J., 85, 2929-2942.
9. Thompson, J.D. et al. (2002). Multiple sequence alignment using Clustalw and Clustalx. Curr. Protoc. Bioinformatics, Chapter 2, Unit 2 3.
10. Wallin, E. and Von Heijne, G. (1998) Genome-wide analysis of integral membrane proteins from Eubacterial, Archaean, and eukaryotic organisms. Protein Sci., 7, 1029-1038.
11. Zachariae, U. et al. (2008) The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure, 16, 747-754.
12. Zhou, Y. et al. (2001) Chemistry of ion coordination and hydration revealed by a K+ channel-Fab complex at 2.0 a resolution. Nature, 414, 43-48.