12.07.2015 Views

From Protein Structure to Function with Bioinformatics.pdf

From Protein Structure to Function with Bioinformatics.pdf

From Protein Structure to Function with Bioinformatics.pdf

SHOW MORE
SHOW LESS

Create successful ePaper yourself

Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.

214 E.C. Meng et al.Bartlett GJ, Borkakoti N, Thorn<strong>to</strong>n JM (2003) Catalysing new reactions during evolution: economyof residues and mechanism. J Mol Biol 331:829–860Berman HM, Westbrook J, Feng Z, et al. (2000) The <strong>Protein</strong> Data Bank. Nucleic Acids Res28:235–242Blow DM, Birk<strong>to</strong>ft JJ, Hartley BS (1969) Role of a buried acid group in the mechanism of actionof chymotrypsin. Nature 221:337–340Bradley P, Kim PS, Berger B (2002) TRILOGY: Discovery of sequence-structure patterns acrossdiverse proteins. Proc Natl Acad Sci USA 99:8500–8505Brakoulias A, Jackson RM (2004) Towards a structural classification of phosphate binding sitesin protein-nucleotide complexes: an au<strong>to</strong>mated all-against-all structural comparison usinggeometric matching. <strong>Protein</strong>s 56:250–260Cammer SA, Hoffman BT, Speir JA, et al. (2003) <strong>Structure</strong>-based active site profiles for genomeanalysis and functional family subclassification. J Mol Biol 334:387–401Chang DT, Weng YZ, Lin JH, et al. (2006) Protemot: prediction of protein binding sites <strong>with</strong>au<strong>to</strong>matically extracted geometrical templates. Nucleic Acids Res 34:W303–309Chen BY, Fofanov VY, Kristensen DM, et al. (2005) Algorithms for structural comparison andstatistical analysis of 3D protein motifs. Pac Symp Biocomput 10:334–345Chen BY, Fofanov VY, Bryant DH, et al. (2007a) The MASH pipeline for protein function predictionand an algorithm for the geometric refinement of 3D motifs. J Comput Biol 14:791–816Chen BY, Bryant DH, Cruess AE, et al. (2007b) Composite motifs integrating multiple proteinstructures increase sensitivity for function prediction. Comput Syst <strong>Bioinformatics</strong> Conf6:343–355Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure inproteins. EMBO J 5:823–826Chothia C, Gough J, Vogel C, et al. (2003) Evolution of the protein reper<strong>to</strong>ire. Science300:1701–1703Devos D, Valencia A (2001) Intrinsic errors in genome annotation. Trends Genet 17:429–431Di Gennaro JA, Siew N, Hoffman BT, et al. (2001) Enhanced functional annotation of proteinsequences via the use of structural descrip<strong>to</strong>rs. J Struct Biol 134:232–245Favia AD, Nobeli I, Glaser F, et al. (2008) Molecular docking for substrate identification: theshort-chain dehydrogenases/reductases. J Mol Biol 375:855–874Fetrow 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 281:949–968Fischer D, Wolfson H, Lin SL, et al. (1994) Three-dimensional, sequence order-independent structuralcomparison of a serine protease against the crystallographic database reveals active sitesimilarities: potential implications <strong>to</strong> evolution and <strong>to</strong> protein folding. <strong>Protein</strong> Sci 3:769–778Glazer DS, Radmer RJ, Altman RB (2008) Combining molecular dynamics and machine learning<strong>to</strong> improve protein function recognition. Pac Symp Biocomput 2008:332–343.Goyal K, Mande SC (2008) Exploiting 3D structural templates for detection of metal-binding sitesin protein structures. <strong>Protein</strong>s 70:1206–1218Goyal K, Mohanty D, Mande SC (2007) PAR-3D: a server <strong>to</strong> predict protein active site residues.Nucleic Acids Res 35:W503–505Hermann JC, Ghanem E, Li Y, et al. (2006) Predicting substrates by docking high-energy intermediates<strong>to</strong> enzyme structures. J Am Chem Soc 128:15882–15891Hermann JC, Marti-Arbona R, Fedorov AA, et al. (2007) <strong>Structure</strong>-based activity prediction foran enzyme of unknown function. Nature 448:775–779International Union of Biochemistry and Molecular Biology: Nomenclature Committee, Webb EC(1992) Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of theInternational Union of Biochemistry and Molecular Biology on the nomenclature and classificationof enzymes. Academic, San Diego, CAIvanisenko VA, Pintus SS, Grigorovich DA, et al. (2004) PDBSiteScan: a program for searchingfor active, binding and posttranslational modification sites in the 3D structures of proteins.Nucleic Acids Res 32:W549–554

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!