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From Protein Structure to Function with Bioinformatics.pdf

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6 <strong>Function</strong> Diversity Within Folds and Superfamilies 165Ojha S, Meng EC, Babbitt PC (2007) Evolution of function in the “Two Dinucleotide BindingDomains” flavoproteins. PLoS Comput Biol 3(7):e121Orengo CA (1999) CORA–<strong>to</strong>pological fingerprints for protein structural families. <strong>Protein</strong> Sci8:699–715Orengo CA, Taylor WR (1996) SSAP: sequential structure alignment program for protein structurecomparison. Method Enzymol 266:617–635Orengo CA, Jones DT, Thorn<strong>to</strong>n JM (1994) <strong>Protein</strong> superfamilies and domain superfolds. Nature372:631–634Orengo CA, Michie AD, Jones S, et al. (1997) CATH–a hierarchic classification of protein domainstructures. <strong>Structure</strong> 5:1093–1108Pegg SC, Brown SD, Ojha S, et al. (2006) Leveraging enzyme structure-function relationships forfunctional inference and experimental design: the structure-function linkage database.Biochemistry 45:2545–2555Piatigorsky J, Kan<strong>to</strong>row M, Gopal-Srivastava R, et al. (1994) Recruitment of enzymes and stressproteins as lens crystallins. EXS 71:241–250Porter CT, Bartlett GJ, Thorn<strong>to</strong>n JM (2004) The Catalytic Site Atlas: a resource of catalytic sitesand residues identified in enzymes using structural data. Nucleic Acids Res 32:D129–D133Redfern OC, Harrison A, Dallman T, et al. (2007) CATHEDRAL: a fast and effective algorithm<strong>to</strong> predict folds and domain boundaries from multidomain protein structures. PLoS ComputBiol 3(11):e232Reeves GA, Dallman TJ, Redfern OC, et al. (2006) Structural diversity of domain superfamiliesin the CATH database. J Mol Biol 360:725–741Reid AJ, Yeats C, Orengo CA (2007) Methods of remote homology detection can be combined <strong>to</strong>increase coverage by 10% in the midnight zone. <strong>Bioinformatics</strong> 23:2353–2360Rison SC, Thorn<strong>to</strong>n JM (2002) Pathway evolution, structurally speaking. Curr Opin Struct Biol12:374–382Rost B (2002) Enzyme function less conserved than anticipated. J Mol Biol 318:595–608Ruepp A, Zollner A, Maier D, et al. (2004) The FunCat, a functional annotation scheme for systematicclassification of proteins from whole genomes. Nucleic Acids Res 32:5539–5545Russell RB, Saqi MA, Sayle RA, et al. (1997) Recognition of analogous and homologous proteinfolds: analysis of sequence and structure conservation. J Mol Biol 269:423–439Russell RB, Sasieni PD, Sternberg MJ (1998) Supersites <strong>with</strong>in superfolds. Binding site similarityin the absence of homology. J Mol Biol 282:903–918Sangar 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> 8:294Shakhnovich BE, Koonin EV (2006) Origins and impact of constraints in evolution of genefamilies. Genome Res 16:1529–1536Shindyalov IN, Bourne PE (1998) <strong>Protein</strong> structure alignment by incremental combina<strong>to</strong>rialextension (CE) of the optimal path. <strong>Protein</strong> Eng 11:739–747Takahashi H, Inagaki E, Kuroishi C, et al. (2004) <strong>Structure</strong> of the Thermus thermophilus putative periplasmicglutamate/glutamine-binding protein. Acta Crystallogr D Biol Crystallogr. 60:1846–1854Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science278:631–637The Gene On<strong>to</strong>logy Consortium (2000) Gene on<strong>to</strong>logy: <strong>to</strong>ol for the unification of biology. NatGenet 25:25–29Tian W, Skolnick J (2003) How well is enzyme function conserved as a function of pairwisesequence identity? J Mol Biol 333:863–882Todd AE, Orengo CA, Thorn<strong>to</strong>n JM (2001) Evolution of function in protein superfamilies, froma structural perspective. J Mol Biol 307:1113–1143Todd AE, Orengo CA, Thorn<strong>to</strong>n JM (2002) Sequence and structural differences between enzymeand nonenzyme homologs. <strong>Structure</strong> 10:1435–1451Whiss<strong>to</strong>ck JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure.Q Rev Biophys 36:307–340

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