From Protein Structure to Function with Bioinformatics.pdf

Index 323Predicting protein-protein interfaces, 183,305, 307Prediction of druggability, 178Preformed structural elements (PSEs), 126, 127Prephenate Dehydratase, 282, 284Principal component analysis (PCA), 223,230–233, 235, 239, 241, 243Principal components, 74, 223, 224, 230–233,239, 241–243Prion, 114, 123, 124, 126, 134Procognate, 145, 158, 159Profile, 10, 27, 35, 36, 40–43, 45–51, 63, 72,76, 77, 96, 101, 106, 120, 171, 188,198, 205, 252, 274, 279, 288Profile-profile alignment, 45, 188, 205ProFunc, 195, 203, 251, 254, 259, 260,262–265, 267–269, 274, 278, 279, 282, 289ProKnow, 195, 203, 251, 253–259, 269, 274Prolinks Database, 254, 255, 258ProMate, 182, 183Propensity-based predictor, 117–118PROSA, 17, 62, 65, 76PROSITE, 173, 255, 257, 258Protein active site, 187, 206Protein Data Bank (PDB)4, 8–10, 12, 17, 20,30, 42, 58, 60, 62, 72, 73, 77, 79, 81,91–94, 96, 102, 103, 120, 123, 147,158, 159, 175, 177, 179, 181, 183, 187,189, 190, 192, 195, 197, 200, 202–205,209, 237, 239, 254–257, 259–261, 263,264, 267, 269, 273, 280–284, 287, 288,295, 298, 303, 304, 306–309, 311, 312Protein fold, 51, 70, 71, 172, 295, 302,303, 306Protein folding, 4, 7, 15, 19, 27, 52, 59, 71,108, 170, 172, 243Protein folding problem, 52, 59, 71Protein function, 7, 80, 113, 128, 144, 145,162, 167–184, 190, 217, 218, 224, 230,233, 235, 242, 244, 267, 274, 288,293–314Protein-ligand interactions, 174, 178, 179Protein-protein interactions, 127, 129,132, 158, 160, 167, 180, 258, 286,305, 307Protein-protein interfaces, 155, 171, 172,180, 183Protein Structure Initiative, 60, 80–81, 278,287, 295, 296, 298Protein structure prediction, 3–20, 28, 30, 32,39, 47, 49, 51, 58–60, 77, 91–108, 295Protemot, 195, 204Proteopedia, 287, 288PSI-BLAST, 41–43, 45, 46, 49, 61, 63, 97,120, 255, 257, 258, 308PSIPRED, 39, 50, 61, 100, 255PSSM, 35, 40, 41, 61QQ-SiteFinder, 176, 177, 181, 183Quasi-harmonic analysis, 230RRandom coil, 114, 118Rapid evolution, 132, 135Reduced alphabet, 121Re-entrant helix, 101, 102Regulation of transcription, 113, 123Remote homology, 38, 41, 42, 44, 50, 147, 151Repeat expansion, 115Repetitive pattern, 115Replica exchange MC method, 14Replica exchange (REX), 228, 243Reverse templates, 203, 264–269, 276, 279,280, 282RIGOR, 195, 200, 203, 208, 255, 256, 258ROSETTA, 6, 7, 9–11, 15, 19, 59, 74, 107,108, 306, 308SSampling performance, 223, 235Sampling problem, 222, 226, 239, 243Scavengers, 124, 125Structural classification of proteins (SCOP),30, 31, 145–147, 150–152, 158, 188,189, 193, 194, 201, 202, 206–209, 280,307–309Secondary structure, 9–12, 18, 35–37, 39–43,47, 66, 67, 72, 75, 77, 106, 108,116–119, 122, 126, 146, 147, 154, 155,184, 197, 198, 208, 237, 255, 266, 268,282, 283, 303, 311Secondary structure indels, 154Secondary Structure Matching (SSM), 39,145, 148, 259–261, 264, 267, 269,279, 280Selectivity, 157, 158, 160, 225, 226, 278Sequence derived properties, 255, 298, 300Sequence family, 81, 151, 152Sequence independence, 132–135Sequence motifs, 98, 115, 127, 128, 149, 188,254, 257, 260, 281Sequence to structure alignment, 65