From Protein Structure to Function with Bioinformatics.pdf

322 IndexLigand-binding templates, 263, 264LIGSITE, 175, 183Linear programming, 38Lipid binding proteins, 310Local similarities, 205, 265, 266, 277, 281Local structure, 20, 51, 126, 187, 188, 205,208, 211, 212Low sequence complexity, 116MMachine learning, 43, 45, 49, 98–104, 119, 182Mad-cow disease, 126Match Augmentation algorithm, 200Match extension, 193Match stringency, 191, 195MCSG. See Midwest Center for StructuralGenomicsMechanistically diverse superfamilies, 155, 162Meta-genomics, 27META-servers, 17, 27, 45, 70Midwest Center for Structural Genomics(MCSG), 254, 259, 267, 278, 282, 284, 285,287, 289MODBASE, 81, 297, 298Model building, 29, 50, 67, 69, 74, 78, 298, 299Model evaluation, 18, 62, 76–77MODELLER, 61, 69, 73, 74, 106Modelling loops, 70–74Model quality, 47, 48, 82, 296, 297Model Quality Assessment Programs(MQAPs), 16, 18, 19, 296Molecular dynamics (MD), 6–9, 13, 15,19, 69, 73–74, 106, 193, 217, 218,220, 226–227, 232–233, 237, 241,243–244Molecular function (MF), 123, 128, 144–145,148–149, 155, 158, 189, 194, 210,258, 278Molecular recognition element (MoRE),127, 129Molecular recognition feature (MoRF),127–130Molecular surface, 168–170, 172, 177, 187,277, 281Molten globule, 114Monte Carlo simulations, 8, 11, 12, 14, 75Motif description and matching, 191Motif discovery, 129, 190, 193, 196, 201,205, 207MSDfold, 279, 280, 282, 283Mucin-binding domain, 307Multiple domain architecture, 156Multiple sequence alignments, 42, 63, 96, 99,100, 103, 171, 182, 278, 280Multiple templates, 64–65, 69, 106, 299NNaive Bayes classifier, 43, 44Natural classification of proteins, 212Neofunctionalisation, 153Nests, 106, 260, 262Neural network, 18, 43–45, 48, 49, 70, 72, 99,117, 119Newton’s equations of motion, 15, 19,218–220, 233, 243Normal mode analysis (NMA), 230, 233,237, 238NP-hard, 34, 35OOrder-promoting amino acid, 131Orthologue, 151, 153, 171, 294, 295, 303PPair-potential, 33, 34, 74PAR-3D, 187, 194, 200, 206Parallel hyperbolic sampling, 14Paralogue, 153, 171PASS, 175, 183Patchfinderplus, 172, 173, 183pdbFun, 194, 204PDBSite database, 194, 203PDBsum, 175, 183, 267, 268PDBsum structural analyses, 267PD-(D/E) XK nuclease, 303–304Periodic boundary conditions, 220Phosphofructokinase (PFK), 310, 311Phosphorylation, 123–125, 131, 258Physics-based energy function, 5–9, 16, 17PINTS, 187, 194, 202, 208PMDB, 297, 298Pocket-finder, 175, 183Poisson Boltzmann equation, 17Polarizable force fields, 220Polarizable water models, 220PONDR, 117, 119, 127, 129, 130Porin, 93, 94, 97Positive and negative examples, 190, 196, 207Positive examples, 131, 190, 193, 196,204–208, 212PPI-Pred, 182, 183Predicting binding site location, 175, 184