From Protein Structure to Function with Bioinformatics.pdf

320 IndexConsensus templates, 205Consurf, 173, 183Convergent evolution, 51, 146, 148, 188, 197,201–203Covariance matrix, 231, 243Critical assessment of structure prediction(CASP), 8, 10, 17, 28, 37, 41, 45, 50,51, 77, 122, 295, 298Cross-validation, 103–105Cupin, 281Cyclin-dependent kinase inhibitor(Cdk), 125, 126DDALI, 145, 147, 148, 255, 258, 279Database of interacting proteins (DIP), 254,255, 258Databases, 4, 30–33, 35, 38, 40–43, 46, 47,51, 52, 58, 61, 68, 69, 71–73, 81, 91,94–98, 102–104, 107, 114, 127,144–147, 151–155, 158, 170, 172–174,179, 181, 194, 195, 197, 200, 202–204,208–210, 254–256, 260, 261, 263, 264,274, 278–280, 287, 288, 294, 297, 298,301–303, 307, 309, 314Databases of 3D motifs, 187, 193–195, 200,202, 203, 207, 213Data sets, 98, 103–105, 107, 259Defrosted approximation, 36De novo modeling. See Ab initio modellingDepth-first searching, 193, 198, 200, 202Directional Atomic Solvation EnergY(DASEY), 255Discovery methods, 190DIscovery of LInear MOTifs(DILIMOT), 129DisEMBL, 117, 118DISOPRED, 117, 120Disorder-promoting amino acid, 131Display site, 124DisProt database, 114Divide and conquer, 373D motifs, 187–213, 256DNA-binding templates, 263, 2643D templates, 63DNase IIα, 312–313Docking, 71, 75, 80, 170, 178, 187, 210–211,218, 281, 296, 301, 302, 309Docking for functional annotation,210–211DRESPAT, 187, 206Drug design, 58, 80, 106, 175, 178, 184, 188,210, 239, 298, 301, 304, 305EEffector, 124, 125, 184Ef-Site, 173, 183Eigenvalue. 232, 238, 243Eigenvector, 223, 224, 231, 232, 235, 238,239, 241, 243Elastic network models (ENM), 238, 244Electrostatic surface properties, 80, 170,172–174, 177, 211, 221, 225, 226, 262,298–300, 308Enhanced sampling methods, 227, 228, 234Ensemble convergence, 235Ensembles, 14, 32, 45, 70, 114, 135, 144, 147,151, 219, 220, 223, 224, 227–235,239–241, 243, 244Entropic chain, 123, 124Entropic spring, 123, 124Enzyme commission (EC) numbers, 57, 144,156, 160, 187, 209, 279, 282, 294Enzyme templates, 263, 282Essential dynamics (ED), 227, 233,234, 243Essential subspace, 229, 232–234, 236Eukaryotic linear motif (ELM), 127, 129European Bioinformatics Institute(EBI), 254, 259Evolution, 34, 51, 58, 69, 106, 113–115, 132,133, 135, 143, 146–148, 152–158, 160,162, 171, 188, 189, 197, 201–203, 212Evolutionary trace method, 171Explicit solvent, 7, 220, 229, 243Exportin, 220Extreme value distribution, 49, 203FFASTA, 61, 63, 259, 265, 282Fold, 3–4, 6, 29, 43, 44, 50–51, 58–62, 67,70–72, 77–78, 81–82, 105, 116, 120,135, 143, 145–150, 154, 161, 162, 171,172, 187, 200, 201, 213, 214, 238,251–256, 258–262, 264, 267, 269, 273,274, 276–280, 285, 286, 295, 306–308,310, 312Fold identification, 62–63, 149FoldIndex, 117, 119Fold matching, 254–256, 259–261, 264, 279Fold recognition, 27–52, 61–62, 64, 77, 81,150, 279, 301–304, 312Fold similarity, 148, 188, 275–277, 280Fold space, 30–31, 147, 162, 171–172, 295,302–303Force field, 6–10, 19–20, 32–34, 60, 68–69,73–74, 120, 219–220, 227, 238, 243, 297