Journal of Computer-Aided Molecular Design, Volume 10

Volume 10, Number 1, February 1996

• Peter D. J. Grootenhuis, Martin Karplus:
  Functionality map analysis of the active site cleft of human thrombin. 1-10
  
• Björn Walse, Magnus Ullner, Christer Lindbladh, Leif Bülow, Torbjörn Drakenberg, Olle Teleman:
  Structure of a cyclic peptide with a catalytic triad, determined by computer simulation and NMR spectroscopy. 11-22
  
• B. G. Rao, E. E. Kim, M. A. Murcko:
  Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods. 23-30
  
• Bernard Pirard, François Durant:
  Molecular modelling and conformational analysis of a GABA_B antagonist. 31-40
  
• Matthias Rarey, Stephan Wefing, Thomas Lengauer:
  Placement of medium-sized molecular fragments into active sites of proteins. 41-54
  
• Laurence Leherte, Thibaud Latour, Daniel P. Vercauteren:
  Similarity and complementarity of molecular shapes: Applicability of a topological analysis approach. 55-66
  
• Carlos Alberto Montanari, M. S. Tute, A. E. Beezer, Julie C. Mitchell:
  Determination of receptor-bound drug conformations by QSAR using flexible fitting to derive a molecular similarity index. 67-73
  
• Maurizio Recanatini:
  Comparative molecular field analysis of non-steroidal aromatase inhibitors related to fadrozole. 74-82
  
• Philippe Hennig, Eric Raimbaud, Christophe Thurieau, Jean-Paul Volland, André Michel, Jean-Luc Fauchère:
  Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin. 83-86
  

Volume 10, Number 2, April 1996

• Barbara Odell, Stephen J. Hammond, Richard Osborne, Michael W. Goosey:
  Conformational and receptor-binding properties of the insect neuropeptide proctolin and its analogues. 89-99
  
• H. Dronia, U. Gruß, G. Hägele, T. Friedrich, H. Weiss:
  Structure-activity analysis of fluorinated 1-N-arylamino-1-arylmethane-phosphonic acid esters as inhibitors of the NADH: ubiquinone oxidoreductase (complex I). 100-106
  
• J. Frau, S. L. Price:
  On the electrostatic and steric similarity of lactam compounds and the natural substrate for bacterial cell-wall biosynthesis. 107-122
  
• Daniel A. Gschwend, Irwin D. Kuntz:
  Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal. 123-132
  
• Qishi Du, Gustavo A. Arteca:
  Modeling lipophilicity from the distribution of electrostatic potential on a molecular surface. 133-144
  
• Supa Hannongbua, Luckhana Lawtrakul, Jumras Limtrakul:
  Structure-activity correlation study of HIV-1 inhibitors: Electronic and molecular parameters. 145-152
  
• Ulf Ryde:
  The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations. 153-164
  
• Soaring Bear, William A. Remers:
  Computer simulation of the binding of amonfide and azonafide to DNA. 165-175
  

Volume 10, Number 3, June 1996

• Pnina Dauber-Osguthorpe, Colette M. Maunder, David J. Osguthorpe:
  Molecular dynamics: Deciphering the data. 177-185
  
• Tudor I. Oprea, Angel E. García:
  Three-dimensional quantitative structure-activity relationships of steroid aromatase inhibitors. 186-200
  
• Wolfgang Brandt, Matthias Stoldt, Heiko Schinke:
  The µ- and delta-opioid pharmacophore conformations of cyclic beta-casomorphin analogues indicate docking of the Phe³ residue to different domains of the opioid receptors. 201-212
  
• Ronald A. Buono, Nathalie Kucharczyk, Magrit Neuenschwander, Johan Kemmink, Lih-Yueh Hwang, Jean-Luc Fauchère, Carol A. Venanzi:
  Synthesis and conformational analysis by ¹H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly]. 213-232
  
• Neil R. Taylor, Mark von Itzstein:
  A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase. 233-246
  
• Frank H. Allen, Stephanie E. Harris, Robin Taylor:
  Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques. 247-254
  
• Daan M. F. van Aalten, Robert P. Bywater, John B. C. Findlay, Manfred Hendlich, Rob W. W. Hooft, Gert Vriend:
  PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. 255-262
  

Volume 10, Number 4, August 1996

• Hans-Joachim Böhm:
  Towards the automatic design of synthetically accessible protein ligands: Peptides, amides and peptidomimetics. 265-272
  
• Mike Carson:
  Wavelets and molecular structure. 273-283
  
• V. Hariprasad, Vithal M. Kulkarni:
  A proposed common spatial pharmacophore and the corresponding active conformations of some peptide leukotriene receptor antagonists. 284-292
  
• Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson:
  Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. 293-304
  
• Christoph A. Sotriffer, Rudolf H. Winger, Klaus R. Liedl, Bernd M. Rode, Janos M. Varga:
  Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4. 305-320
  
• Ricardo L. Mancera:
  Towards an understanding of the molecular basis of hydrophobicity. 321-326
  
• Peng Gao:
  Comparison of cyclic delta-opioid peptides with non-peptide delta-agonist spiroindanyloxymorphone (SIOM) using the message-address concept: A molecular modeling study. 327-336
  
• David E. Clark, David R. Westhead:
  Evolutionary algorithms in computer-aided molecular design. 337-358
  

Volume 10, Number 5, October 1996

• Ernest V. Curto, Hunter N. B. Moseley, N. Rama Krishna:
  CORCEMA evaluation of the potential role of intermolecular transferred NOESY in the characterization of ligand-receptor complexes. 361-371
  
• Amedeo Caflisch:
  Computational combinatorial ligand design: Application to human alpha-thrombin. 372-396
  
• David E. Clark, David R. Westhead, Richard A. Sykes, Christopher W. Murray:
  Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits. 397-416
  
• J. G. Vinter:
  Extend electron distributions applied to the molecular mechanics of some intermolecular interactions. II. Organic complexes. 417-426
  
• Ajay N. Jain:
  Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. 427-440
  
• Yitbarek H. Mariam, Alesia Sawyer:
  A computational study on the relative reactivity of reductively activated 1, 4-benzoquinone and its isoelectronic analogs. 441-460
  
• Paul H. J. Nederkoorn, Joop H. van Lenthe, Henk van der Goot, Gabriëlle M. Donné-Op den Kelder, Henk Timmerman:
  The agonistic binding site at the histamine H₂ receptor. I. Theoretical investigations of histamine binding to an oligopeptide mimicking a part of the fifth transmembrane alpha-helix. 461-478
  
• Paul H. J. Nederkoorn, Erna M. van Gelder, Gabriëlle M. Donné-Op den Kelder, Henk Timmerman:
  The agonistic binding site at the histamine H₂ receptor. II. Theoretical investigations of histamine binding to receptor models of the seven alpha-helical transmembrane domain. 479-489
  
• Mattia Falconi, Ruggero Gallimbeni, Emanuele Paci:
  Dimer asymmetry in superoxide dismutase studied by molecular dynamics simulation. 490-498
  

Volume 10, Number 6, December 1996

• David Chapman:
  The measurement of molecular diversity: A three-dimensional approach. 501-512
  
• Glen Eugene Kellogg, Lemont B. Kier, Patrick Gaillard, Lowell H. Hall:
  E-state fields: Applications to 3D QSAR. 513-520
  
• Soheila Anzali, Gerhard Barnickel, Michael Krug, Jens Sadowski, Markus Wagener, Johann Gasteiger, Jaroslaw Polanski:
  The comparison of geometric and electronic properties of molecular surfaces by neural networks: Application to the analysis of corticosteroid-binding globulin activity of steroids. 521-534
  
• Begoña Hernández, Modesto Orozco, F. Javier Luque:
  Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase. 535-544
  
• John B. Bremner, Burak Coban, Renate Griffith:
  Pharmacophore development for antagonists at alpha₁ adrenergic receptor subtypes. 545-557
  
• Yoriko Iwata, Atsushi Kasuya, Shuichi Miyamoto:
  Reconstruction of the 3D coordinates of alpha-carbon atoms of proteins from a pair of stereographic figures. 558-566
  
• Laura Belvisi, Gianpaolo Bravi, Giovanna Catalano, Massimo Mabilia, Aldo Salimbeni, Carlo Scolastico:
  A 3D QSAR CoMFA study of non-peptide angiotensin II receptor antagonists. 567-582
  
• Stanislaw Oldziej, Jerzy Ciarkowski:
  Mechanism of action of aspartic proteinases: Application of transition-state analogue theory. 583-588
  
• Elizabeth Yuriev, John D. Orbell:
  Modelling steric effects in DNA-binding platinum(II)-am(m)ine complexes. 589-606
  
• J. E. J. Mills, Philip M. Dean:
  Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. 607-622
  
• John H. Van Drie:
  An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility. 623-630
  

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