INDEX A E Accessible surface area (ASA) ..................... 113, 117, 126 Enzyme commission number (EC) .................. 44, 47, 48 Allostery.........................................................................108 Artificial neural network (ANN) ..............................61–62 G Aspartate transcarbamoylase (ATCase).......................181, Gene ontology (GO) ............................44, 47, 48, 53, 54 182, 184 Glycoprotein................................................................9, 10 Atg13 .................................................................. 51, 52, 54 Guanylate kinase........................................................53, 55 Atg101.......................................................................50–52 H B Haematopoetic cell kinase ................................... 114, 115 Binding affinity...............................................98, 100, 101 High-throughput screening .................................. 93, 108 Binding site.......................................................... 1, 3, 4, 7, HIV-1 protease .............................................................100 66, 78, 82–84, 92, 119, 214 Homology .........................................................29, 37, 38, Biotechnology ........................................................ 71, 131 63, 65, 66, 76, 92, 102, 164, 170, 171, 190 Bovine beta-trypsin .............................133, 135, 136, 141 HORMA domain ......................................................50–54 C J Cα-Cα distance....................................................... 30, 166 Jupyter notebook ........................................ 217, 229, 237 Catalytic triad ..................................................... 29, 68–70 Chemical shift............................................. 147, 188–190, K 192–196, 200, 202, 204, 205, 208–210, 212–216, 230, 237, 242, 245–250 Karplus equation .................................................. 230, 246 CMTI-I................................................133, 135, 136, 141 L Coarse-grained simulation.......................... 222, 235, 236 Cryo-electronmicroscopy(cryo-EM) ................. 123–129, Legionella pneumophila................................................... 29 145–161, 170–172 M D Maximum entropy ............................................... 219–238 Dendrogram ...................................................... 17, 20–22, Molecular dynamics ........................................18, 98, 108, 25, 30, 37, 41 111, 118, 124, 148–150, 220, 241–243 Distance matrix ............................................................... 37 restrained ........................................................ 150, 241 Distance restraint ................................................ 147–149, Multiple sequence alignment ............................ 17, 44, 47 171, 172, 207, 230, 243–245, 253 Docker .................................................................... 16, 242 N Docking .............................................................92, 94, 95, Nipah virus G glycoprotein ........................................9, 10 98, 107–110, 112–115, 117, 118, 132–136, Normal mode analysis..................................15, 18, 24–26 139–142, 146–161, 164, 165, 167–168, 170, 172 Nuclear magnetic resonance (NMR) rigid-body ......................................134, 140, 142, 147 spectroscopy............................................. 188, 219, Domain..........................................................4, 29–33, 37, 229, 241, 243 43–56, 165, 166, 168, 172, 190, 192, 234, 235 NMR-STAR format ............................................ 190, 191, Drug-target complex ....................................................107 193–195, 197–199, 211, 213, 243–245 DSSP............................................................ 32, 33, 39, 42 Zolta´ nGa´ spa´ ri (ed.), Structural Bioinformatics: Methods and Protocols, Methods in Molecular Biology, vol. 2112, https://doi.org/10.1007/978-1-0716-0270-6, © Springer Science+Business Media, LLC, part of Springer Nature 2020 255 STRUCTURAL BIOINFORMATICS:METHODS AND PROTOCOLS 256 Index Nuclear Overhauser effect (NOE) ..................... 192, 196, Rotation matrix ............................................134, 177–179 200, 206, 207, 209, 222, 228, 230, 232, 233, RuvA DNA helicase ........................................................ 45 237, 238, 243–246, 248 S P Secondary structure element .................... 21, 32–34, 176 Partial charge.........................................33, 109, 118, 119 Shigella flexneri 2a.........................................................235 Parvulin-type peptidyl proline isomerases ...................249 Sialidase-2 ........................................................................ 96 P-loop NTPase ................................................................ 55 Simulated annealing.....................................132, 148–150 Principal component analysis (PCA).......................15–17, Small angle X-ray scattering ............................... 131, 132, 23–26, 28, 249–251 134, 136, 138–142, 221, 222, 230, 233–238 Protein Data Bank (PDB) ............................ 2–4, 6, 8–10, SMILES .....................................................................92, 96 12, 16, 18, 19, 22, 23, 26–29, 32, 33, 36, 37, 39, Staphylococcus aureus .....................................................249 41, 43, 44, 46, 50–55, 63, 66, 68, 70, 79, 92, 94, Statistical potential ....................................................60–61 96, 98, 102, 107, 109, 110, 112–115, 136, 142, Structural ensemble ............................................. 241–254 146, 153–155, 159, 169, 175, 182, 184, 188, Structural similarity...........................................18, 24, 30, 192, 199, 206, 230, 242–244 31, 38, 76, 175 Protein design ..............................................60, 66–68, 72 Structure alignment ........................................... 34, 44, 47 Protein dynamics...........................................................241 Structure superposition ..................................... 15, 21–23 Protein-ligand Superfamily........................................................44, 45, 47, docking ................................................................94, 98 48, 50, 52–55 interaction.................................................................. 18 Protein-protein T docking .......................................................... 132, 136, Transmembrane region........................................ 123–129 146, 165, 167 TRIc/CCT chaperonin.................................................171 interaction...............................................131–142, 214 3D Symbol Nomenclature for Graphical Representation interface ........................................................ 76, 79, 81 of Glycans (3D-SNFG) .................................4, 5, 9 Protein sf3636...............................................................235 PrsA................................................................................249 U Puu algorithm ................................................................. 32 UniProt...................................................... 1, 2, 4, 66, 126 R V Rhizomucor miehei ..................................................68–72 Ribose-binding protein (RBPs)......................... 18, 23–26 van der Waals radius.............................................. 76, 138, Ribosome............................................................... 94, 150, 149, 150 155–159, 179 Virtual screening .......................................................92–94 Ricin................................................................................. 94 X RNA polymerase II ............................................. 165, 166, 168, 169, 172 X-ray crystallography .....................................65, 107, 146 Root mean square deviation (RMSD) .............17, 21, 22, 25, 26, 30, 38, 53, 76, 141, 150, 158–161, 166, Z 168, 169, 178–182, 184, 233, 246 Zanamivir......................................................................... 96 Rossmann fold................................................................. 68.