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From Protein Structure to Function with Bioinformatics.pdf

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88 A. FiserPetrey D, Xiang Z, Tang CL, et al. (2003) Using multiple structure alignments, fast model building,and energetic analysis in fold recognition and homology modeling. <strong>Protein</strong>s 53(Suppl6):430–435Pieper U, Eswar N, Davis FP, et al. (2006) MODBASE: a database of annotated comparative proteinstructure models and associated resources. Nucleic Acids Res 34:D291–295Pillardy J, Czaplewski C, Liwo A, et al. (2001) Recent improvements in prediction of proteinstructure by global optimization of a potential energy function. Proc Natl Acad Sci USA98:2329–23233Qian B, Ortiz AR, Baker D (2004) Improvement of comparative model accuracy by free-energyoptimization along principal components of natural structural variation. Proc Natl Acad SciUSA 101:15346–15351Rai BK, Fiser A (2006) Multiple mapping method: a novel approach <strong>to</strong> the sequence-<strong>to</strong>-structurealignment problem in comparative protein structure modeling. <strong>Protein</strong>s 63:644–661Rai BK, Madrid-Aliste CJ, Fajardo JE, et al. (2006) MMM: a sequence-<strong>to</strong>-structure alignmentpro<strong>to</strong>col. <strong>Bioinformatics</strong> 22:2691–2692Reddy BV, Li WW, Shindyalov IN, et al. (2001) Conserved key amino acid positions (CKAAPs)derived from the analysis of common substructures in proteins. <strong>Protein</strong>s 42:148–163Ring CS, Cohen FE (1993) Modeling protein structures: construction and their applications.FASEB J 7:783–890Ring CS, Sun E, McKerrow JH, et al. (1993) <strong>Structure</strong>-based inhibi<strong>to</strong>r design by using proteinmodels for the development of antiparasitic agents. Proc Natl Acad Sci USA 90:3583–3587Rohl CA, Strauss CE, Chivian D, et al. (2004) Modeling structurally variable regions in homologousproteins <strong>with</strong> rosetta. <strong>Protein</strong>s 55:656–677.Rost B (1997) <strong>Protein</strong> structures sustain evolutionary drift. Fold Des 2:S19–S24Rost B (1999) Twilight zone of protein sequence alignments. <strong>Protein</strong> Eng 12:85–94Rudolph MG, Stanfield RL, Wilson IA (2006) How TCRs bind MHCs, peptides, and corecep<strong>to</strong>rs.Annu Rev Immunol 24:419–466Rusch DB, Halpern AL, Sut<strong>to</strong>n G, et al. (2007) The Sorcerer II Global Ocean Sampling expedition:northwest Atlantic through eastern tropical Pacific. PLoS Biol 5:e77Rychlewski L, Jaroszewski L, Li W, et al. (2000) Comparison of sequence profiles. Strategies forstructural predictions using sequence information. <strong>Protein</strong> Sci 9:232–241Rykunov D, Fiser A (2007) Effects of amino acid composition, finite size of proteins, and sparsestatistics on distance-dependent statistical pair potentials. <strong>Protein</strong>s 67:559–568Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints.J Mol Biol 234:779–815Sali A, Matsumo<strong>to</strong> R, McNeil HP, et al. (1993) Three-dimensional models of four mouse mast cellchymases. Identification of proteoglycan binding regions and protease-specific antigenicepi<strong>to</strong>pes. J Biol Chem 268:9023–9034Sali A, Shakhnovich E, Karplus M (1994) How does a protein fold? Nature 369:248–251Samudrala R, Moult J (1998) A graph-theoretic algorithm for comparative modeling of proteinstructure. J Mol Biol 279:287–302Sanchez R, Sali A (1997) Evaluation of comparative protein structure modeling by MODELLER-3. <strong>Protein</strong>s(Suppl 1):50–58Sanchez R, Sali A (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiaegenome. Proc Natl Acad Sci USA 95:13597–13602Sangar V, Blankenberg DJ, Altman N, et al. (2007) Quantitative sequence-function relationshipsin proteins based on gene on<strong>to</strong>logy. BMC <strong>Bioinformatics</strong> 8:294Saraste M, Sibbald PR, Wittinghofer A (1990) The P-loop–a common motif in ATP- and GTPbindingproteins. Trends Biochem Sci 15:430–434Sauder JM, Arthur JW, Dunbrack RL, Jr. (2000) Large-scale comparison of protein sequencealignment algorithms <strong>with</strong> structure alignments. <strong>Protein</strong>s 40:6–22Schaffer AA, Aravind L, Madden TL, et al. (2001) Improving the accuracy of PSI-BLAST proteindatabase searches <strong>with</strong> composition-based statistics and other refinements. Nucleic Acids Res29:2994–3005

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