From Protein Structure to Function with Bioinformatics.pdf
From Protein Structure to Function with Bioinformatics.pdf
From Protein Structure to Function with Bioinformatics.pdf
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12 Prediction of <strong>Protein</strong> <strong>Function</strong> from Theoretical Models 315Bujnicki JM (2003) Crystallographic and bioinformatic studies on restriction endonucleases:inference of evolutionary relationships in the “midnight zone” of homology. Curr <strong>Protein</strong> PeptSci 4:327–337Bumbaca D, Littlejohn JE, Nayakanti H, et al. (2007) Genome-based identification and characterizationof a putative mucin-binding protein from the surface of Strep<strong>to</strong>coccus pneumoniae.<strong>Protein</strong>s 66:547–558Cammer SA, Hoffman BT, Speir JA, et al. (2003) <strong>Structure</strong>-based active site profiles for genomeanalysis and functional family subclassification. J Mol Biol 334:387–401Castrignano T, De Meo PD, Cozzet<strong>to</strong> D, et al. (2006) The PMDB <strong>Protein</strong> Model Database.Nucleic Acids Res 34:D306–309Chakravarty S, Sanchez R (2004) Systematic analysis of added-value in simple comparative modelsof protein structure. <strong>Structure</strong> 12:1461–1470Chakravarty S, Wang L, Sanchez R (2005) Accuracy of structure-derived properties in simplecomparative models of protein structures. Nucleic Acids Res 33:244–259Chi A, Kemp RG (2000) The primordial high energy compound: ATP or inorganic pyrophosphate?J Biol Chem 275:35677–35679Cymerman IA, Meiss G, Bujnicki JM (2005) DNase II is a member of the phospholipase D superfamily.<strong>Bioinformatics</strong> 21:3959–3962Davis FP, Braberg H, Shen MY, et al. (2006) <strong>Protein</strong> complex compositions predicted by structuralsimilarity. Nucleic Acids Res 34:2943–2952Davis FP, Barkan DT, Eswar N, et al. (2007) Host pathogen protein interactions predicted bycomparative modeling. <strong>Protein</strong> Sci 16:2585–2596Feder M, Bujnicki JM (2005) Identification of a new family of putative PD-(D/E)XK nucleases<strong>with</strong> unusual phylogenomic distribution and a new type of the active site. BMC Genomics6:21Fetrow JS, Skolnick J (1998) Method for prediction of protein function from sequence using thesequence-<strong>to</strong>-structure-<strong>to</strong>-function paradigm <strong>with</strong> application <strong>to</strong> glutaredoxins/thioredoxins andT1 ribonucleases. J Mol Biol 281:949–968Fetrow JS, Godzik A, Skolnick J (1998) <strong>Function</strong>al analysis of the Escherichia coli genome usingthe sequence-<strong>to</strong>-structure-<strong>to</strong>-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxindisulfide oxidoreductase activity. J Mol Biol 282:703–711Furnham N, Ruffle S, Southan C (2004) Splice variants: a homology modeling approach. <strong>Protein</strong>s54:596–608Hattersley AT, Ashcroft FM (2005) Activating mutations in Kir6.2 and neonatal diabetes: newclinical syndromes, new scientific insights, and new therapy. Diabetes 54:2503–2513Hermann JC, Marti-Arbona R, Fedorov AA, et al. (2007) <strong>Structure</strong>-based activity prediction foran enzyme of unknown function. Nature 448:775–779Jacobson M, Sali A (2004) Comparative protein <strong>Structure</strong> Modelling and its applications <strong>to</strong> drugdiscovery. Annu Rep Med Chem 39:259–274Jordan IK, Wolf YI, Koonin EV (2004) Duplicated genes evolve slower than single<strong>to</strong>ns despitethe initial rate increase. BMC Evol Biol 4:22Kolinski A, Bujnicki JM (2005) Generalized protein structure prediction based on combination offold-recognition <strong>with</strong> de novo folding and evaluation of models. <strong>Protein</strong>s 61(Suppl 7):84–90Kopp J, Schwede T (2004) The SWISS-MODEL Reposi<strong>to</strong>ry of annotated three-dimensional proteinstructure homology models. Nucleic Acids Res 32:D230–234Krishnamurthy N, Brown D, Sjolander K (2007) FlowerPower: clustering proteins in<strong>to</strong> domain architectureclasses for phylogenomic inference of protein function. BMC Evol Biol 7(Suppl 1):S12Kryshtafovych A, Venclovas C, Fidelis K, et al. (2005) Progress over the first decade of CASPexperiments. <strong>Protein</strong>s 61(Suppl 7):225–236Kryshtafovych A, Fidelis K, Moult J (2007) Progress from CASP6 <strong>to</strong> CASP7. <strong>Protein</strong>s 69(Suppl8):194–207Lopez C, Chevalier N, Hannaert V, et al. (2002) Leishmania donovani phosphofruc<strong>to</strong>kinase. Genecharacterization, biochemical properties and structure-modeling studies. Eur J Biochem269:3978–3989