From Protein Structure to Function with Bioinformatics.pdf
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From Protein Structure to Function with Bioinformatics.pdf
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4 Membrane <strong>Protein</strong> <strong>Structure</strong> Prediction 109Ghosh S, Liu XP, Zheng Y, et al. (2001) Rational design of potent and selective EGFR tyrosinekinase inhibi<strong>to</strong>rs as anticancer agents. Curr Cancer Drug Targets 1:129–140Gromiha MM, Ponnuswamy PK (1993) Prediction of transmembrane beta-strands from hydrophobiccharacteristics of proteins. Int J Pept <strong>Protein</strong> Res 42:420–431Gromiha MM, Ahmad S, Suwa M (2004) Neural network-based prediction of transmembranebeta-strand segments in outer membrane proteins. J Comput Chem 25:762–767Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc NatlAcad Sci USA 89:10915–10919Higgins D, Thompson J, Gibson T, et al. (1994) CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penaltiesand weight matrix choice. Nucleic Acids Res 22:4673–4680Horn F, Bettler E, Oliveira L, et al. (2003) GPCRDB information system for G protein-coupledrecep<strong>to</strong>rs. Nucleic Acids Res 31:294–297Jacoboni I, Martelli PL, Fariselli P, et al. (2001) Prediction of the transmembrane regions ofbeta-barrel membrane proteins <strong>with</strong> a neural network-based predic<strong>to</strong>r. <strong>Protein</strong> Sci10:779–787Jayasinghe S, Hris<strong>to</strong>va K, White SH (2001) MP<strong>to</strong>po: a database of membrane protein <strong>to</strong>pology.<strong>Protein</strong> Sci 10:455–458Jones DT (2001) Predicting novel protein folds by using FRAGFOLD. <strong>Protein</strong>s 5:127–132Jones DT (2007) Improving the accuracy of transmembrane protein <strong>to</strong>pology prediction usingevolutionary information. <strong>Bioinformatics</strong> 23:538–544Jones DT, Taylor WR, Thorn<strong>to</strong>n JM (1994a) A model recognition approach <strong>to</strong> the prediction ofall-helical membrane protein structure and <strong>to</strong>pology. Biochemsitry 33:3038–3049Jones DT, Taylor WR, Thorn<strong>to</strong>n JM (1994b) A mutation data matrix for transmembrane proteins.FEBS Lett 339:269–275Klabunde T, Hessler G (2002) Drug design strategies for targeting G-protein-coupled recep<strong>to</strong>rs.ChemBioChem 3:928–944Koehl P, Delarue M (1996) Mean-field minimization methods for biological macromolecules.Curr Opin Struct Biol 6:222–226Krogh A, Larsson B, von Heijne G, et al. (2001) Predicting transmembrane protein <strong>to</strong>pology <strong>with</strong>a hidden Markov model: application <strong>to</strong> complete genomes. J Mol Biol 305:567–580Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein.J Mol Biol 157:105–132Kyttälä A, Ihrke G, Vesa J, et al. (2004) Two motifs target Batten disease protein CLN3 <strong>to</strong> lysosomesin transfected nonneuronal and neuronal cells. Mol Biol Cell 15:1313–1323Käll L, Krogh A, Sonnhammer E (2004) A combined transmembrane <strong>to</strong>pology and signal peptideprediction method. J Mol Biol 338:1027–1036Käll L, Krogh A, Sonnhammer E (2005) An HMM posterior decoder for sequence feature predictionthat includes homology information. <strong>Bioinformatics</strong> 21:251–257Li B, Gallin WJ (2004) VKCDB: voltage-gated potassium channel database. BMC <strong>Bioinformatics</strong> 5:3Liu Q, Zhu YS, Wang BH, et al. (2003) A HMM-based method <strong>to</strong> predict the transmembraneregions of beta-barrel membrane proteins. Comput Biol Chem 27:69–76Lo A, Chiu HS, Sung TY, et al. (2008) Enhanced membrane protein <strong>to</strong>pology prediction using ahierarchical classification method and a new scoring function. J Proteome Res 7:487–496Lomize AL, Pogozheva ID, Lomize MA, et al. (2006a) Positioning of proteins in membranes: acomputational approach. <strong>Protein</strong> Sci 15:1318–1333Lomize MA, Lomize AL, Pogozheva ID, et al. (2006b) OPM: orientations of proteins in membranesdatabase. <strong>Bioinformatics</strong> 22:623–625Mahajan S, Ghosh S, Sudbeck EA, et al. (1999) Rational design and synthesis of a novel antileukemicagent targeting Bru<strong>to</strong>n’s tyrosine kinase (BTK), LFM-A13. J Biol Chem274:9587–9599Mao Q, Foster BJ, Xia H, et al. (2003) Membrane <strong>to</strong>pology of CLN3, the protein underlyingBatten disease. FEBS Lett 541:40–46