From Protein Structure to Function with Bioinformatics.pdf

2 Fold Recognition 55Tress ML, Jones D, Valencia A (2003) Predicting reliable regions in protein alignments fromsequence profiles. J Mol Biol 330:705–718Venclovas C, Margelevicius M (2005) Comparative modeling in CASP6 using consensusapproach to template selection, sequence-structure alignment, and structure assessment.Proteins(Suppl 7):99–105Wallner B, Elofsson A (2005) Pcons5: combining consensus, structural evaluation and fold recognitionscores. Bioinformatics 21:4248–4254Wallner B, Elofsson A (2006) Dentification of correct regions in protein models using structural,alignment, and consensus information. Prot Sci 15:900–913Westhead DR, Collura VP, Eldridge MD, et al. (1995) Protein fold recognition by threading:comparison of algorithms and analysis of results. Protein Eng 8:1197–1204Weston J, Elisseeff A, Zhou D, et al. (2004) Protein ranking: from local to global structure in theprotein similarity network. PNAS 101:6559–6563Xia Y, Levitt M (2000) Extracting knowledge-based energy functions from protein structures byerror rate minimization. Comparison of methods using lattice model. J Chem Phys113:9318–9330Xu J, Li M, Kim D, et al. (2003) RAPTOR: optimal protein threading by linear programming.J Bioinform Comput Biol 1:95–117Xu Y, Xu D, Uberbacher EC (1998) An efficient computational method for globally optimalthreading. J Comput Biol 5:597–614Zachariah MA, Crooks GE, Holbrook SR, Brenner SE (2005) A generalized affine gap modelsignificantly improves protein sequence alignment accuracy. Proteins 58:329–338Zhang Y (2007) Template-based modeling and free modeling by I-TASSER in CASP7.Proteins(Suppl 8):108–117Zhang Y, Skolnick J (2005) The protein structure prediction problem could be solved using thecurrent PDB library. Proc Natl Acad Sci USA 102:1029–1034Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolutionand from depth-dependent structural alignment of fragments. Proteins 58:321–328