From Protein Structure to Function with Bioinformatics.pdf

54 L.A. KelleyLathrop RH, Smith TF (1996) Global optimum protein threading with gapped alignment andempirical pair potentials. J Mol Biol 255:641–665Leslie C, Eskin E, Noble WS (2002) The spectrum kernel: a string kernel for SVM protein classification.Pac Symp Biocomput 564–575Leslie CS, Eskin E, Cohen A, et al. (2004) Mismatch string kernels for discriminative proteinclassification. Bioinformatics 20:467–476Liao L, Noble WS (2003) Combining pairwise sequence similarity and support vector machinesfor detecting remote protein evolutionary and structural relationships. J Comput Biol10:857–868Madej T, Gilbrat J-F, Bryant SH (1995) Threading a database of protein cores. Proteins23:356–369Marsden RL, Lee D, Maibaum M, et al. (2006) Comprehensive genome analysis of 203 genomesprovides structural genomics with new insights into protein family space. Nucleic Acids Res34:1066–1080McGuffin LJ (2008) The ModFOLD server for the quality assessment of protein structural models.Bioinformatics 24:586–587Miyazawa S, Jernigan RL (1996) Residue-residue potentials with a favorable contact pair termand an unfavorable high packing density term, for simulation and threading. J Mol Biol256(3):623–644Moult J, Fidelis K, Kryshtafovych A, et al. (2007) Critical assessment of methods of proteinstructure prediction - Round VII. Proteins 69 S8:3–9Murzin AG, Brenner SE, Hubbard T, et al. (1995) SCOP: a structural classification of proteinsdatabase for the investigation of sequences and structures. J Mol Biol 247:536–540Nguyen MN, Rajapakse JC (2003) Multi-class support vector machines for protein secondarystructure prediction. Genome Inform Ser Workshop Genome Inform 14:218–227Ohlson T, Wallner B, Elofsson A (2004) Profile-profile methods provide improved fold-recognition:a study of different profile-profile alignment methods. Proteins 57:188–197Park J, Teichmann SA, Hubbard T, et al. (1997) Intermediate sequences increase the detection ofhomology between sequences. J Mol Biol 273:349–354Pearson WR (1998) Empirical statistical estimates for sequence similarity searches. J Mol Biol276:71–84Ponting CP, Russell RB (2000) Identification of distant homologues of fibroblast growth factorssuggests a common ancestor for all beta-trefoil proteins. J Mol Biol 302:1041–1047Prasad JC, Vajda S, Camacho CJ (2004) Consensus alignment server for reliable comparativemodeling with distant templates. Nucleic Acids Res 32:W50–W54Richmond TJ (1984) Solvent accessible surface area and excluded volume in proteins. Analyticalequations for overlapping spheres and implications for the hydrophobic effect. J Mol Biol178:63–89Rychlewski L, Jaroszewski L, Li W, Godzik A (2000) Comparison of sequence profiles. Strategiesfor structural predictions using sequence information. Protein Sci 9:232–241Science Editorial (2005) So much more to know. Science 309:78–102Seringhaus M, Gerstein M (2007) Chemistry Nobel rich in structure. Science 315:40–41Sippl MJ (1990) Calculation of conformational ensembles from potentials of mean force. Anapproach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol213:859–883Skolnick J, Kihara D (2000) Defrosting the frozen approximation: PROSPECTOR - a newapproach to threading. Proteins 42:319–331Soeding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics21:951–960Tanaka S, Scheraga HA (1976) Medium- and long-range interaction parameters between aminoacids for predicting three-dimensional structures of proteins. Macromolecules 9:945–950Tang CL, Xie L, Koh IY, et al. (2003) On the role of structural information in remote homologydetection and sequence alignment: new methods using hybrid sequence profiles. J Mol Biol334:1043–1062