From Protein Structure to Function with Bioinformatics.pdf

Index 321Fragment search approach to loop modelling,71–73Free energy landscape, 228, 234–235Free modeling. See Ab initio modellingFrozen approximation, 36FSSP, 147, 255FunClust, 194, 206,Functional annotation, 57, 71, 78, 82,143, 146, 148, 151, 154, 188–189,210–211, 252–253, 255, 258–259,273, 280, 289, 294Functional family, 151, 160Functional modes, 220, 227, 237–238, 244Functional sites, 71, 149, 172, 202, 205–206,209, 262, 295, 300–301Function prediction, 132–133, 147–151, 162,169, 171–172, 174, 183–184, 203, 210,251–269, 273–289, 293–294, 296,300–302, 306–307, 309, 314Fuzziness, 133–134Fuzzy functional forms, 187, 198, 300GGASPS, 187, 194, 207Gaussian network models, 238Gene3D, 152Gene duplication, 152–153, 157, 294–295Gene Ontology (GO), 122–123, 128, 144–145,187–189, 194–195, 203, 208–209,253–255, 257–259, 306, 308–309biological process (BP), 91, 123, 128,144–145, 189, 226, 253, 258cellular localization (CL), 123, 306molecular function (MF), 123, 128,144–145, 148–149, 155, 158, 189,194, 208, 210, 258, 278Generalized ensemble, 14, 228–229, 234, 243Genetic algorithms, 8, 15, 69, 73, 207Geometrical constraints, 233, 239, 244,Geometric hashing, 191, 197–198, 208Geometric sieving, 207Gibbs Sampling, 37, 49Global similarities, 279, 281. See also FoldmatchingGlobPlot, 117Graph theory methods, 192GRID, 179Hessian matrix, 238Het Group, 263Het Group Dictionary, 263Hidden Markov Models (HMM), 41–42, 45,47–49, 63, 99–101, 151–152, 252Histone, 134Homology, 29, 38, 39, 41, 42, 44–47, 50–52,60, 68, 101, 103–105, 143, 147–152,162, 172, 197, 210, 211, 257, 296, 305Homology modeling. See ComparativemodellingHomology network, 27, 45, 46HotPatch, 174Hot-spot residues in protein interfaces, 181Hybrid (Point-Surface) descriptions, 208Hydrophobic cluster analysis, 118Hydrophobicity, 75, 96–99, 102, 115, 117,118, 169, 170, 174, 182, 226, 301Hydrophobic surface, 172,Hypothetical protein, 253, 275, 278–280IImplicit solvent, 7, 220, 227, 243Integer programming, 38Integration, 75, 226, 289Interactome, 125Intermediate sequence search, 41, 45InterProScan, 259, 260Intrinsically disordered protein (IDP),113–135Intrinsically disordered region (IDR), 122,123, 125, 127Intrinsically unstructured protein (IUP), 114IUPred, 117, 120I-TASSER, 6, 12, 13, 19, 49, 50, 61, 308JJESS, 194, 195, 198, 201, 203, 263KKinetic trapping, 228Knowledge-based energy function, 5, 9, 10,16, 17Knowledge-based potential, 8, 9, 17, 18, 20,32, 35, 179HHaem oxygenase, 280Hamiltonian REX, 228Helix-turn-helix (HTH) motif, 260, 261, 285LLeap-frog algorithm, 219Ligand binding, 71, 174–176, 178, 183, 184,194, 195, 203, 212, 297