From Protein Structure to Function with Bioinformatics.pdf

90 A. Fiservan Vlijmen HW, Karplus M (1997) PDB-based protein loop prediction: parameters for selectionand methods for optimization. J Mol Biol 267:975–1001Venclovas C, Margelevicius M (2005) Comparative modeling in CASP6 using consensusapproach to template selection, sequence-structure alignment, and structure assessment.Proteins 61:99–105.Venter JC, Remington K, Heidelberg JF, et al. (2004) Environmental genome shotgun sequencingof the Sargasso Sea. Science 304:66–74Vernal J, Fiser A, Sali A, et al. (2002) Probing the specificity of a trypanosomal aromatic alphahydroxyacid dehydrogenase by site-directed mutagenesis. Biochem Biophys Res Commun293:633–639Vitkup D, Melamud E, Moult J, et al. (2001) Completeness in structural genomics. Nat Struct Biol8:559–566Wallner B, Elofsson A (2005a) Pcons5: combining consensus, structural evaluation and fold recognitionscores. Bioinformatics 21:4248–4254Wallner B, Elofsson A (2005b) All are not equal: a benchmark of different homology modelingprograms. Protein Sci 14:1315–1327Wallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Pconsand ProQ. Proteins 69(Suppl 8):184–193Wallner B, Larsson P, Elofsson A (2007) Pcons.net: protein structure prediction meta server.Nucleic Acids Res 35:W369–374Wlodawer A, Miller M, Jaskolski M, et al. (1989) Conserved folding in retroviral proteases: crystalstructure of a synthetic HIV-1 protease. Science 245:616–621Wu CH, Apweiler R, Bairoch A, et al. (2006) The Universal Protein Resource (UniProt): anexpanding universe of protein information. Nucleic Acids Res 34:D187–191Wu G, Fiser A, ter Kuile B, et al. (1999) Convergent evolution of Trichomonas vaginalis lactatedehydrogenase from malate dehydrogenase. Proc Natl Acad Sci USA 96:6285–6290Wu G, McArthur AG, Fiser A, et al. (2000) Core histones of the amitochondriate protist, Giardialamblia. Mol Biol Evol 17:1156–1163Xiang Z, Soto CS, Honig B (2002) Evaluating conformational free energies: The colony energyand its application to the problem of loop prediction. Proc Natl Acad Sci USA99:7432–7437Xiao H, Verdier-Pinard P, Fernandez-Fuentes N, et al. (2006) Insights into the mechanism ofmicrotubule stabilization by Taxol. Proc Natl Acad Sci USA 103:10166–10173Xu J, Jiao F, Yu L (2007) Protein structure prediction using threading. Methods Mol Biol413:91–122Xu LZ, Sanchez R, Sali A, et al. (1996) Ligand specificity of brain lipid-binding protein. J BiolChem 271:24711–24719Yooseph S, Sutton G, Rusch DB, et al. (2007) The Sorcerer II Global Ocean Sampling expedition:expanding the universe of protein families. PLoS Biol 5:e16Zhang C, Liu S, Zhou Y (2004) Accurate and efficient loop selections by the DFIRE-based allatomstatistical potential. Protein Sci 13:391–399Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7. Proteins69(Suppl 8):108–117Zheng Q, Rosenfeld R, Vajda S, et al. (1993) Determining protein loop conformation using scaling-relaxationtechniques. Protein Sci 2:1242–1248Zhou H, Pandit SB, Lee SY, et al. (2007) Analysis of TASSER-based CASP7 protein structureprediction results. Proteins 69(Suppl 8):90–97