From Protein Structure to Function with Bioinformatics.pdf

4 Membrane Protein Structure Prediction 111Taylor PD, Attwood TK, Flower DR (2003) BPROMPT: a consensus server for membrane proteinprediction. Nucleic Acids Res 31:3698–3700Tusnády GE, Simon I (1998) Principles governing amino acid composition of integral membraneproteins: application to topology prediction. J Mol Biol 283:489–506Tusnády GE, Dosztányi Z, Simon I (2005a) TMDET: web server for detecting transmembraneregions of proteins by using their 3D coordinates. Bioinformatics 21:1276–1277Tusnády GE, Dosztányi Z, Simon I (2005b) PDB_TM: selection and membrane localization oftransmembrane proteins in the protein data bank. Nucleic Acids Res. 33:275–278Tusnády GE, Kalmár L, Simon I (2008) TOPDB: topology data bank of transmembrane proteins.Nucleic Acids Res 36:234–239Viklund H, Elofsson A (2008) OCTOPUS: improving topology prediction by two-track ANNbasedpreference scores and an extended topological grammar. Bioinformatics 24:1662–1668Viklund H, Granseth E, Elofsson A (2006) Structural classification and prediction of reentrantregions in alpha-helical transmembrane proteins: application to complete genomes. J Mol Biol361:591–603Wallin E, Tsukihara T, Yoshikawa S, et al. (1997) Architecture of helix bundle membrane proteins:an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci 6:808–815Wallner B, Elofsson A (2005) Pcons5: combining consensus, structural evaluation and fold recognitionscores. Protein Sci 14:1315–1327White S (2004) The progress of membrane protein structure determination. Protein Sci13:1948–1949Wimley WC (2003) The versatile beta-barrel membrane protein. Curr Opin Struct Biol13:404–411Wimley WC, White SH (1996) Experimentally determined hydrophobicity scale for proteins atmembrane interfaces. Nat Struct Biol 3:842–848Yarov-Yarovoy V, Baker D, Catterall WA (2006) Voltage sensor conformations in the open andclosed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci USA103:7292–7297Yuan Z, Mattick JS, Teasdale RD (2004) SVMtm: support vector machines to predict transmembranesegments. J Comput Chem 25:632–636von Heijne G (1992) Membrane protein structure prediction. Hydrophobicity analysis and thepositive-inside rule. J Mol Biol 225:487–494