Table Of Content

Journal of MOLECULAR GRAPHICS VOLUME 10, 1992 AUTHOR/TITLE INDEX Abraham, D. J.: See Kellogg, G. E., 212 Gilbert, R. J. Protein structure prediction from Automated site-directed drug design using Adzhubei, A. A.: See Vassylyev, D. G., 101 predicted residue properties utilizing a molecular lattices, 66 Aqvist, J. and Tapia, O. A molecular model digital encoding algorithm, 112 Lim, H. A.: See Kuznetsov, D. A., 25 for the retinol binding protein-transthyretin Good, A. C. The calculation of molecular complex, 120 similarity: alternative formulas, data Maigret, B.: See Pattou, D., 241 Arnold, J.: See Dolata, D. P., 222 manipulation and graphical display, 144 Mhin, B. J.: See Kim, S., 218 Goodsell, D. S. and Olson, A. J. Molecular Morimoto, Y.: See Fujii, 1., 185 Bach, L. H.: See Pattou, D., 241 illustration in black and white, 235 Mornon, J. P.: See Badel, A., 205 Badel, A., Mornon, J. P. and Hazout, S. Mullier, G. W.: See Taylor, R., 152 Searching for geometric molecular shape Haaksma, E. E. J., Donné-Op den Kelder, G. complementarity using bidimensional M., Vernooijs, P. and Timmerman, H. A surface profiles, 205 Oldfield, T. J. SQUID: A program for the theoretical study concerning the mode of Banaszak, L. J.: See Levitt, D. G., 229 analysis and display of data from interaction of the histamine H,-agonist Brunie, S.: See Demaret, J.-P., 257 crystallography and molecular dynamics, dimaprit, 79 247 Hazout, S.: See Badel, A., 205 Chun, P. W. and Jou, W. S. Molecular Olson, A. J.: See Goodsell, D. S., 235 Higuchi, Y.: See Fujii, I., 185 conformation of ubiquitinated structures and Osguthorpe, D. J. and Dauber-Osguthorpe, P. Huang, C.: See Lewis, R. A., 66 the implications for regulatory function, 7 FOCUS: a program for analyzing molecular Hybl, A. and Gaber, B. P. Using a RIBBON Clark, D. E., Willett, P. and Kenny, P. W. dynamics simulations, featuring digital program to illustrate lipid bilayer packing, Pharmacophoric pattern matching in files of signal-processing techniques, 178 253 three-dimensional chemical structures: use of bounded distance matrices for the Pattou, D., Bach, L. H., Kocher, J. P. and representation and searching of Jou, W. S.: See Chun, P. W., 7 Maigret, B.M OL3D—A modular and conformationally flexible molecules, 194 interactive program for molecular modeling Cognet, J. A. H.: See Gabarro-Arpa, J., 166 Kellogg, G. E. and Abraham, D. J. KEY, and conformational analysis: If. Extended LOCK, and LOCKSMITH: Complementary modules, 241 Dauber-Osguthorpe, P.: See Osguthorpe, D. hydropathic map predictions of drug Pickover, C. A. DNA and protein tetragrams: J., 178 structure from a known receptor-receptor Biological sequences as tetrahedral de la Cruz, X., Reverter, J. and Fita, I. structure from known drugs, 212 movements, 2 Representation of noncovalent interactions Kenny, P. W.: See Clark, D. E., 194 Presentations from the Molecular Graphics in protein structures, 96 Kim, H. S.: See Kim, S., 218 Society Meeting, 35 Delaney, J. S. Finding and filling protein Kim, K. S.: See Kim, S., 218 cavities using cellular logic operations, 174 Kim, S., Yoon, C. W., Mhin, B. J., Kim, H. Demaret, J.-P. and Brunie, S. A unique Reverter, J.: See de la Cruz, X., 96 S. and Kim, K. S. Photorealistic image structural feature of a phospholipase A, is Richards, W. G. Editorial: Names and Logos, generation of molecular structure on PC probed by molecular dynamics, 257 130 screen using the ray-tracing technique, 218 Dolata, D. P. and Arnold, J. An easily fixed Roe, D. C.: See Lewis, R. A., 66 Kocher, J. P.: See Pattou, D., 241 error in the Nyburg algorithm for Kuntz, I. D.: See Lewis, R. A., 66 discovering the best fit between molecules, Kuznetsov, D. A. and Lim, H. A. VisiCoor: Salemme, F. R.: See Wendoloski, J. J., 124 222 A simple program for visualization of Sander, C.: See Tuparev, G., 12 Donné-Op den Kelder, G. M.: See Haaksma, proteins, 25 Sexton, G. J.: See Taylor, R., 152 E. EB. F., 79 Shibata, M. and Zielinski, T. J. Computer graphics presentations and analysis of Ferrin, T. E.: See Lewis, R. A., 66 Laaksonen, L. A graphics program for the hydrogen bonds from molecular dynamics Fita, I.: See de la Cruz, X., 96 analysis and display of molecular dynamics simulation, 88 Fujii, I., Morimoto, Y., Higuchi, Y. and trajectories, 33 Yasuoka, N. XELE—a polypeptide model- Langridge, R.: See Lewis, R. A., 66 building program for a graphics Le Bret, M.: See Gabarro-Arpa, J., 166 Tapia, O.: See Aqvist, J., 120 workstation, 185 Levitt, D. G. and Banaszak, L. J. POCKET: Taylor, R., Mullier, G. W. and Sexton, G. J. A computer graphics method for identifying Automation of conformational analysis and Gabarro-Arpa, J., Cognet, J. A. H. and Le and displaying protein cavities and their other molecular modeling calculations, 152 Bret, M. Object Command Language: a surrounding amino acids, 229 Timmerman, H.: See Haaksma, E. E. J., 79 formalism to build molecular models and to Lewis, R. A. Automated site-directed drug- Tuparev, G., Vriend, G. and Sander, C. GCI: analyze structural parameters in design: a method for the generation of A network server for interactive 3D macromolecules, with applications to general three-dimensional molecular graphs, graphics, 12 nucleic acids, 166 131 Turner, D. C. and Gaber, B. P. A Gaber, B. P.: See Hybl, A., 253; Turner, D. Lewis, R. A., Roe, D. C., Huang, C., Ferrin, crystallographic molecular lattice builder €.,23 T. E., Langridge, R. and Kuntz, I. D. applied to model lipid bilayers, 29 J. Mol. Graphics, 1992, Vol. 10, December 261 Vassylyev, D. G. and Adzhubei, A. A. Wendoloski, J. J. and Salemme, F. R. Yasuoka, N.: See Fujii, 1., 185 Tek_FRODO: A new version of FRODO PROBIT: A statistical approach to modeling Yoon, C. W.: See Kim, S., 218 for Tektronix graphics stations, 101 proteins from partial coordinate data using Vernooijs, P.: See Haaksma, E. E. J., 79 substructure libraries, 124 Zielinski, T. J.: See Shibata, M., 88 Vriend, G.: See Tuparev, G., 12 Willett, P.: See Clark, D. E., 194 KEYWORDS INDEX Allostery, 212 Frequency distribution, 178 PC, 218 AMBER, 241 FRODO, 101 Pharmacophoric pattern matching, 194 Analysis, 247 Phospholipase A,, 257 Animation, 33 Geometric search, 194 Polypeptide model-building, 185 Graphical analysis, 144 Program, 247 Base pair, 88 Graphics, 247 Programming language, 166 Protein, 25, 229 BBBeiislntad yienrfgi,t, , 222922 29 HH,,--argeocneipst; to,r , 7799 : PPrrootteeiinn ccarvyisttiaelsl, ogr1a7p4h y, 185 BBoouunndd eds modoitsthainncge, ma1t9r4i x, 194 HHHiiIgsNhtT-a,lm eivne2el1, 2 m7o9d eling language, 152 PPPrrrooottteeeiiinnn -pdsreeosqtiuegeinnn, c esi1,n2t 4er 2a ction, 120 HIV-1 protease, 66 Protein structure, 101 Cambridge Crystallographic Database, 241 Homology building, 124 Protein structure prediction, 112 Cambridge Structural Database, 152 Hydrocarbon graphical representations, 253 Publication graphics, 235 Cellular logic, 174 Hydropathy, 2? Characteristic modes, 178 Hydrophobicity, 212 QSAR, 212 Complementarity, 212 Ray-tracing, 218 Complex formation, 205 Illustrating polymethylene chains, 253 Retinol binding protein, 120 Computer graphics, 33 Isosurface model, 185 Computer modeling, 124 Rotamers, 124 Conformational analysis, 152 Line drawing, 235 Conformational flexibility, 194 Lipid, 29 Screen search, 194 Conformational search, 194 Lipid ribbon models, 253 Secondary structure, 25 Conformational space analysis, 33 Secondary structure prediction, 112 Crystal, 29 Section complementarity, 205 Crystallographic refinement, 101 Macromolecular structure parameters, 166 Selective optimization, 144 Matching pattern, 205 Similarity indices, 144 Membrane, 29 Solid filling, 174 Database searching, 66 Message passing, 12 Stability of protein conformations, 96 Data processing, 247 MidaPlus, 66 Steric differences, 144 Dimaprit, 79 MM2, 241 _ . Structure, 212 2-dimensional image processing, 235 Molecular dynamics, 33, 178, 247, 257 Structure-activity relationships, 241 3-D graphics server, 12 Molecular dynamics simulation, 88 Structure evaluation, 124 Distance geometry, 194 Molecular graphics, 12, 25, 66, 166, 218 Structure generation, 66, 131 DNA sequences, 2 Molecular graphs, 131 Supersecondary structure, 25 Docking, 241 Molecular illustration, 235 Surface, 229 Drawings of bilayers, 253 Molecular mechanics, 166, 178, 257 Surface fractality, 120 Drug design, 66, 131 Molecular model binding, 166 Ducking, 229 Molecular modeling, 101, 241, 257 Tektronix, 101 Molecular surface, 205 Tetragrams, 2 MOPAC, 241 Three-center hydrogen bond, 88 EGA, 218 Torsion angle fitting, 131 Electron density, 185 Noncovalent interactions in protein structures, Electrostatic potential, 144 96 22 Ubiquitinated structures, 7 staicundianel Nyburg, 222 Unusual hydrogen bond, 88 Flip-flop hydrogen bond, 88 Pattern matching, 112 VGA, 218 Fourier transforms, 178 Pattern recognition, 174 Free energy of solvation, 96 Patterns and sequences, 2 Watson-Crick hydrogen bond, 88 262 J. Mol. Graphics, 1992, Vol. 10, December eSaeeelwaieeOegetng e n ,