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112, 115 Ab Initio Methods 76 Ab Initio Modeling 55 Abiotic 447 Absorption 591 Index “1.13.12.4” 112, 115 additivity schemes 56–58, 62f, 70 adenosine monophosphate (AMP) a 121–123 ab initio methods 76 adipose 240 ab initio modeling 55 ADME (absorption, distribution, abiotic 447 metabolism and excretion) 272, absorption 5, 135, 178, 240, 333, 359 333, 359, 448 acceptor 16, 68, 118, 178, 181, 190, ADME-Tox 166, 178ff, 272, 350–353, 249, 263, 264, 269, 270, 279, 299, 544 301, 302, 318, 322, 347, 428, 453 adrenaline 261 see also hydrogen-bond ADRIANA-Code 338–347 acceptors adverse drug reactions (ADRs) 398 accessibility 101, 182, 210, 285, 292, aem-thiolate proteins 366 367, 516 Aerococcus viridans, 128 accessible surface area 294 aflatoxin 445 ACD/MS Fragmenter 151, 375 Aggregated Computational Toxicology ACD software 143, 156 Resource (ACToR) 431 ACD structure elucidator 154, 155 agonists 167, 225, 361, 375 acetylcholinesterase inhibitors 418 agricultural research 417ff Achilles project 198, 199 agrochemical industry 6, 313 acid dissociation constant (pKa) 54, air-water contact angle 553 73–76, 349, 456 alanine 95, 128 acidity 11, 53, 456 albumin 349, 350 activation energy 121 alcohol and aldehyde dehydrogenases active analog approach 263 363 active pharmaceutical ingredients aldehydes 175, 363, 378, 511 (APIs) 453, 573 aldose reductase-2 (ALR-2) 240 active sites 179, 283–292, 298–304, algorithmic complexity 268 315, 317, 367 alignment 24 activity cliffs 320 multiple sequence 285, 291, 298 ADABoost 26 structure 178 adaptive neuro-fuzzy inference system alignment-independent 3D QSAR (ANFIS) 350, 352 methods 24 adaptive soft sensors 576–578, 582 aliphatic carboxylic acids 73, 75 Applied Chemoinformatics: Achievements and Future Opportunities, First Edition. Edited by Thomas Engel and Johann Gasteiger. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA. Published 2018 by Wiley-VCH Verlag GmbH & Co. KGaA. 592 Index Allen scheme 62 anti-wrinkles/anti-ageing 538 allosteric sites 284 apoprotein 428 allosterism 413 applicability domain (AD) 32, 41–43, Almond 24 46, 66, 334, 365 ALOGP 57, 65 application programming interface ALOGPS 65f (API) 449 alpha-hydroxy-isocaproate 126 APROPOS 287 alpha shapes 287 AQUASOL 342 ALR2 inhibitors 240, 242 aqueous solubility (log S) see water alternating least squares (ALS) 492 solubility (log S) AM1, 66, 367 archazolide A (ArcA) 224 AMBER 319 ARChem-Route Designer,99 Ames test 432 Arctander atlas 512 p-aminobenzenesulfonamides 260 arctigenin 226 -amino-phenylpropanoicmimic 242 area under the curve (AUC) 46, 326, amorphous forms 55, 69–72 483 -amylase 275 arene oxide formation 381 -amylase inhibitor 276 arginine (Arg98) 424 anaerobic gut bacteria 362 aromatic systems 57, 63, 136, 145, 184, analytical chemistry 7, 469–493 263, 265–266, 318, 374, 381, 419, animal studies 188, 429, 441 507 anisotropy 144, 149 aromaticity 55, 252, 460 annotated genomes 123, 125 Artemisinin 115f annotations 198 artificial intelligence 5, 134, 413 active site 293 artificial neural network (ANN) 17f, binding site 284 28f, 135, 138, 154, 227, 335, 338, antagonism 260 478, 492, 555 antagonist 167, 260, 275, 361, 369, 409, artificial neural network ensembles 413 (ANNE) 350, 352 anti-cancer effects 224 ASN.1 format 250 ant colony optimization (ACO) 316, Aspirin 254 492 assay 209, 247 anti-inflammation 535, 538 assay ID (AID) identifier 247 anti-inflammatory compounds 221, assay-to-lead attrition 178 224, 227, 240, 373 ASSEMBLE 153 anti-influenza 226 assertional metadata 397 antibacterial treatment 125 assertion re-generation 397 antibiotics 170 associative neural networks (ASNN) antibody markers 565 145 anticonvulsant effect 514–516 Asteraceae, 227f antidepressant 517 atom-based contribution method 57, antipsychotic agent 374 60 antitarget 220 atom-centered code 136 anti-T2D compound database (ADB) atom counts 250, 507–509 239 atomic electronegativity distance vector anti-T2D drug target 238 (VAED) 139 antiviral agents 272 atomic properties 56, 135, 338 Index 593 atomic resolution 110, 112 binding motif 323 atom-to-atom matching 110, 252 binding pocket 179–181, 189, 221, attribute selection 124 225, 226, 428 attrition 166, 178, 183 binding pose 209, 230, 316, 425, 428 autocorrelation 16, 173, 177, 186, 346 Bingo 449 autocorrelation vectors 16, 338 binned nearest neighbors (BNN) 483 AutoDock 221, 315f bioactivation 361f automated interpretation 135 bioactive polymers 561–564 automated synthesis design 102 bioactivity 13, 198f, 211, 226, 361, automated text mining 398 395f automatic information extraction 77 bioassays 240 automatic knowledge extraction 151 bioavailability 63, 209, 274, 293, 333, automatic recognition 150 336, 353 autoscaling 472 biochemical assay 418, 431 average absolute error (AAE) 70, 337 biochemical databases 375 Ayurveda 171 biochemical on-chip assay 408 biochemical pathways 106–115, 566 b biochemical reactions 85, 106, 110, back-propagation 29 125, 171 error 492 biochemical synthesis 375 neural network (NN) 65f, 154 biocompatibility 551 backward-elimination regression 21 BioCyc 111 bagged decision tree (BDT) 346, 347, biodegradation 533 349, 480 biodistribution 413 bagging 26, 346, 480 biodiversity 208 baicalein 221 bioinformatics 2, 108, 123, 125, 166, base learners 25f 168, 170, 195, 407, 527 baseline toxicity 185 biological activities 10, 11, 17, 18, 190, basis set 476 408, 442–44 Bayes’ rule 577 biological affinity 361 Bayes’ theorem 28 biological analogs 448 Bayesian methods 552, 554 biological data 14, 20, 25, 166, 229, 553 Bayesian regularized artificial neural biological testing of matching molecules network (BRANN) 29 272 Beilstein Handbook 96 biology files 386 benchmarking 66, 210 biology-oriented synthesis (BIOS) 209, Benson scheme 61 412 benzodiazepine agonists (BDA) 173, biomarker 128, 195, 199 174 biomolecules databases 505 benzoic acid 456, 457 BioPath.Database 109–128 benzyloxybenzene 418 BioSM 375 beta-secretase 408 biotechnology 175, 246, 313 big data 77, 413, 495, 549 biotic 447 binary classification 45, 347, 397 biotransformation 359, 361, 362, 368 bindability 292, 294 BIOVIA Direct 449 binding affinity 69, 181, 210, 265, 317, BitterDB 505, 509 319, 320 bitvectors 251f 594 Index BLAST 297f CASPER program 144 BLASTP 126 CAST 286, 287 bleaching 418 catalysts 263, 278, 549, 554, 558 BLOCKS 298 catalytic cycle 366 blood–brain barrier (BBB) 334, catalytic site 275, 283, 365 342–346 catechol 381 Boehm’s function 320 CATH 298 Boltzmann’s equation 419 CavBase 299, 301 bond additivity 62 CCR8, 408 bond angle strain 63 CDK 449 bond-type E-state descriptors 65 CDK2 complex 268, 270, 297 Boolean array 15 cDNA microarray analysis 536 boosted trees 480, 487 cell boosting 26 adhesion 533, 535, 551 bootstrapping 31, 37–38, 45, 294, 491 communication 534 breast cancer drug 87 extracellular matrix interactions 534 BRENDA 126 migration 534 brewing 511 proliferation 536 broker model 200 cellular and molecular processes 106, BSAlign 301 536 building blocks 240, 391, 409, 412 cellular disease models 199 Center for Food Safety and Applied c Nutrition (CFSAN) 443, 506 Caco-2 cell line 350 centering 19, 472 Caco-2 cell permeability 349, 350 central metabolism 106, 108 CACTVS 387, 389–391 central nervous system (CNS) 172, 342 CADEX method 35, 36 ceramics 554 calibration 11, 320, 486 Cerius2, 347 Cambridge Structural Database 319, cetirizine 73 390 Chamming 27 CAMEO program 97 charge density 55 cancer 87, 196, 198, 199, 386, 445, 518, charge distribution 24, 248, 507 556 CHARGE program 144 cancer cell line encyclopedia (CCLE) ChEBI database 111, 112 199 CheMagic.org 388 canonical variables 479 Chematica 100–101 carbinolamine 378–381 ChemAxon 400, 449 carbocyclic coformycin 122, 123 ChemBank 198 carbohydrates 106, 505 ChEMBL database 13, 196, 198, 395 carcinogenicity 336, 429, 431, 434, ChemDraw/SymxyDraw 253 435, 442, 443 Chemical Abstract Services (CAS) 386 Carcinogenic Potency Database Chemical Abstracts 96, 255, 386 (CPDBAS) 434 Chemical Activity Predictor (CAP) cardiotoxicity 350 391 Cartesian coordinates 135, 137 chemical descriptors, see descriptors Case Ultra 430 chemical environment effect 135, 136, CAS numbers 253 141, 149, 293, 301, 338, 367 Index 595 chemical identifier resolver (CIR) models 11 387–388 random forest 293 chemical information 3, 134, 137, 168, supervised 479 385, 506, 511 classification and regression trees chemical properties 5, 10, 11, 53, 135, (CART) 480 300, 587 click chemistry 90 chemical reactors 572 clinical trials 188, 219, 549 chemical shifts 136, 141–149 clique detection 299, 301, 316 chemical space 34, 95, 171, 292, 322, Cliquer 301 334, 365, 462–464, 506–510, 549 CLOGP 65, 347 Chemical Structure Lookup Service cluster(ing) 17, 27, 36, 293, 397, 447 (CSLS) 388, 389 analysis 150, 477 chemical subgraphs and reaction genome 123–125, 129 mark-up language (CSRML) hierarchical 124, 270 453, 457 structure-based 430 chemical systems biology 125, 588 cluster-based methods 35, 36 CHEMICS 153 COCOA 154 ChemInform 99 CODESSA 555 ChemNavigator iResearchTM, 391 coenzyme Q10, 486 ChemOffice 143, 144 co-factors 121, 266, 360, 363, 364, 427 chemogenomics 171, 199 cohesive energy 558 chemome 239 collision-induced dissociation (CID) chemometrics 2, 17, 471–496 151 chemoselectivity 92–93, 360 column distillation 579–581 ChemoText 399, 400 combinatorial chemistry 53, 134, 141, ChemoTyper 58, 187, 188, 454 166, 175 chemotypes 187, 239, 240–243, 445, combinatorial libraries 172, 175, 183, 453–459 513 ChemScore 320 COMBINE program 153 ChemSpider project 14, 256, 400 CoMFA 22–25, 181 Chinese herbal medicine 172, 221, comparative molecular field analysis 237–243 (CoMFA) 22, 365, 420, 421 CHIRON computer program
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