From Protein Structure to Function with Bioinformatics.pdf

324 IndexStructure-function linkage database (SFLD),145, 150, 152, 155–157Sharp2, 182, 183Short Linear Motif Discovery (SliMDisc), 129Short linear motif (SLiM), 97, 127, 129Shwachman-Bodian-Diamond syndrome,285, 286Signal peptide, 99–101, 105, 129Signal transduction, 92, 113, 114, 123, 128,144, 218Simulated annealing, 14, 37, 69, 73, 107Simulated tempering, 228Simulation methodology, 218Single-point-centred descriptions, 208Singular-value decomposition, 230SOIPPA, 188, 205Solvation potential, 17, 18, 32, 73Solvent accessible surface, 168–170SPASM, 188, 199, 200, 203, 207Specificity diverse superfamilies, 157, 160SpoVS, 308Statistical significance, 47–49, 187, 196,200–202, 205, 206, 208, 209Structural embellishments, 155, 282Structural genomics (SG), 27, 58, 60, 78, 81,113, 143, 147, 149, 152, 167, 171, 188,189, 209, 211, 251, 254, 259, 273–289,293, 295, 302, 307Structural homology, 151, 162Structural templates, 51, 72, 190, 201, 302Structure comparison, 148, 205, 308Structure decoys, 5, 12, 17, 19Structure-function paradigm, 113, 114Structure prediction, 3–20, 28, 30, 32, 39, 41,43, 45, 47, 49, 51, 52, 58, 59, 77, 81,91–108, 116, 122, 126, 230, 295, 303,304, 308, 309Structure refinement, 7–9, 15Subfunctionalisation, 153Sub-optimal alignment, 48SuMo, 195, 203Superfamily, 30, 71, 95–97, 143–162, 189, 190,192–195, 199–201, 206–208, 211, 260,281, 282, 303, 307–309, 313Superfamily motifs, 199Superfolds, 149, 150, 152Supersites, 149, 150SuperStar, 179Support vector machines, 43, 44, 47, 49, 100,102, 103, 117, 120, 128, 178Surface conservation, 171, 173Surface properties, 167–184, 298, 300Surfnet, 175, 183, 262SWISS-MODEL, 62, 81, 106, 297, 298TT4-lysozyme, 222–224TASSER, 6, 7, 12, 17, 19tCONCOORD, 239, 241TEE-REX, 229, 234–237, 243Template-based modelling (TBM), 4, 10, 12,19, 59, 60, 106. See also ComparativemodellingTemplate-free modeling. See Ab initiomodellingTemplates, 4, 8, 10, 12, 18, 19, 29, 30, 35–37,39–43, 45, 47, 48, 50, 51, 58–72,74–76, 78–81, 96, 105, 106, 188, 190,194, 198, 201, 203, 205, 260, 262–267,269, 273, 276, 279, 280, 282, 283, 293,295–302, 304, 306, 308, 309, 312Template search methods, 63, 65Template selection, 64, 69, 78, 106THEMATICS, 177, 183THREADER, 37Threading, 12, 17, 18, 27, 31–38, 41, 42,45, 48–51, 59, 61, 63, 65, 67, 75, 255,305, 308TOPSAN, 287Transcription factor, 123, 124, 128, 131–134,170, 308Transition pathway, 235–237Transmembrane protein, 93–95, 97, 98Tumor suppressor p53, 114, 119,126, 130UUbiquitination, 124, 125Undirected mining, 190, 201, 202UniProt, 4, 258, 260, 264, 297User-Defined Motifs, 194, 196,197, 202Vvan der Waals surface, 167–169Verify3d, 18, 62, 65, 70, 76WWater permeation, 225Whole genome analysis, 100, 102, 103Wiki, 287XX-ray crystallography, 58, 60, 77, 79, 81, 114,217, 222, 233