Journal of Computer-Aided Molecular Design, Volume 12

Volume 12, Number 1, January 1998

• Gerhard Müller, Henry Giera:
  Protein secondary structure templates derived from bioactive natural products - Combinatorial chemistry meets structure-based design. 1-6
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• Nuria B. Centeno, Juan J. Perez:
  A proposed bioactive conformation of Peptide T. 7-14
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• Anderson Coser Gaudio, Yuji Takahata, William Graham Richards:
  Prediction of the binding mode of N2-phenylguanine derivative inhibitors to herpes simplex virus type 1 thymidine kinase. 15-25
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• Tomas Hansson, John Marelius, Johan Åqvist:
  Ligand binding affinity prediction by linear interaction energy methods. 27-35
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• Paul R. Gerber:
  Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB. 37-51
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• Mischa L. M. Beckers, Willem J. Melssen, Lutgarde M. C. Buydens:
  Predicting nucleic acid torsion angle values using artificial neural networks. 53-61
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• Sanja Tomic, Razif R. Gabdoulline, Biserka Kojic-Prodic, Rebecca C. Wade:
  Classification of auxin plant hormones by interaction property similarity indices. 63-79
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• Jonas Nilsson, Evert J. Homan, Age K. Smilde, Cor J. Grol, Håkan Wikstrüm:
  A multiway 3D QSAR analysis of a series of (S)-N-[(1-ethyl-2-pyrrolidinyl)methyl]-6-methoxybenzamides. 81-93
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Volume 12, Number 2, March 1998

• Roy J. Vaz, Larry R. McLean, John T. Pelton:
  Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-amidino-2-naphthyl)propanoic acid hydrochloride and some analogs to Factor Xa using a comparative molecular field analysis. 99-110
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• Marta Filizola, Juan J. Perez, Maria Cartenì-Farina:
  BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors. 111-118
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• John Marelius, Malin Graffner-Nordberg, Tomas Hansson, Anders Hallberg, Johan Åqvist:
  Computation of affinity and selectivity: Binding of 2, 4-diaminopteridine and 2, 4-diaminoquinazoline inhibitors to dihydrofolate reductases. 119-131
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• Traian Sulea, Ludovic Kurunczi, Tudor I. Oprea, Zeno Simon:
  MTD-ADJ: A multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities. 133-146
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• Samuel Petit, Frédéric Brard, Gérard Coquerel, Guy Perez, François Tron:
  Structural models of antibody variable fragments: A method for investigating binding mechanisms. 147-163
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• John R. Woolfrey, Mitchell A. Avery, Arthur M. Doweyko:
  Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis. 165-181
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• Marcel J. de Groot, Remco W. A. Havenith, H. Maarten Vinkers, Renate Zwaans, Nico P. E. Vermeulen, Joop H. van Lenthe:
  Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s. 183-193
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• Louis Carlacci:
  Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations. 195-213
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Volume 12, Number 3, May 1998

• Randall J. Radmer, Peter A. Kollman:
  The application of three approximate free energy calculations methods to structure based ligand design: Trypsin and its complex with inhibitors. 215-227
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• Anton V. Filikov, Thomas L. James:
  Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein. 229-240
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• Fabio Zuccotto, Andrew C. R. Martin, Roman A. Laskowski, Janet M. Thornton, Ian H. Gilbert:
  Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania. 241-257
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• Carlos Alemán, Jordi Casanovas, Sérgio E. Galembeck:
  PAPQMD parametrization of molecular systems with cyclopropyl rings: Conformational study of homopeptides constituted by 1-aminocyclopropane-1-carboxylic acid. 259-273
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• Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski:
  Molecular modeling of the human vasopressin V2 receptor/agonist complex. 275-287
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• André H. Juffer, Hans J. Vogel:
  A flexible triangulation method to describe the solvent-accessible surface of biopolymers. 289-299
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• Martti Ovaska, Ari Yliniemelä:
  A semiempirical study on inhibition of catechol O-methyltransferase by substituted catechols. 301-307
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Volume 12, Number 4, July 1998

• Hans-Joachim Böhm:
  Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs. 309-323
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• Andrey A. Bliznyuk, Jill E. Gready:
  Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase. 325-333
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• Nikolay P. Todorov, Philip M. Dean:
  A branch-and-bound method for optimal atom-type assignment in de novo ligand design. 335-349
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• M. Paulino, A. Esteves, M. Vega, G. Tabares, R. Ehrlich, O. Tapia:
  Modelling a 3D structure for EgDf1 from shape Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand. 351-360
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• Paola Fossa, Raffaella Boggia, Luisa Mosti:
  Toward the identification of the cardiac cGMP inhibited-phosphodiesterase catalytic site. 361-372
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• Divi Venkateswarlu, Jerzy Leszczynski:
  Tautomeric equilibria in 8-oxopurines: Implications for mutagenicity. 373-382
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• Jonas Boström, Per-Ola Norrby, Tommy Liljefors:
  Conformational energy penalties of protein-bound ligands. 383-396
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• Somsak Tonmunphean, Sirirat Kokpol, Vudhichai Parasuk, Peter Wolschann, Rudolf H. Winger, Klaus R. Liedl, Bernd M. Rode:
  Comparative molecular field analysis of artemisinin derivatives: Ab initio versus semiempirical optimized structures. 397-409
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Volume 12, Number 5, September 1998

• Mary Troconis, Wenwen Ma, David E. Nichols, Jerry McLaughlin:
  Molecular modeling study of tubulosine and other related ipecac alkaloids. 411-418
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• Jin-Soo Song, Heungrok Park, Hyo-Jeong Hong, Myeong-Hee Yu, Seong-Eon Ryu:
  Homology modeling of the receptor binding domain of human thrombopoietin. 419-424
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• Michael Meyer, Gerd Wohlfahrt, Jörg Knäblein, Dietmar Schomburg:
  Aspects of the mechanism of catalysis of glucose oxidase: A docking, molecular mechanics and quantum chemical study. 425-440
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• Camden A. Parks, Gordon M. Crippen, John G. Topliss:
  The measurement of molecular diversity by receptor site interaction simulation. 441-449
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• Qishi Du, Paul G. Mezey:
  Heuristic lipophilicity potential for computer-aided rational drug design: Optimizations of screening functions and parameters. 451-470
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• Matthias Rarey, J. Scott Dixon:
  Feature trees: A new molecular similarity measure based on tree matching. 471-490
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• Christian Lemmen, Claus Hiller, Thomas Lengauer:
  RigFit: A new approach to superimposing ligand molecules. 491-502
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• Christopher W. Murray, Timothy R. Auton, Matthew D. Eldridge:
  Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. 503-519
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Volume 12, Number 6, November 1998

• Ian J. Bruno, Jason C. Cole, Jos P. M. Lommerse, R. Scott Rowland, Robin Taylor, Marcel L. Verdonk:
  IsoStar: A library of information about nonbonded interactions. 525-537
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• Wynn L. Walker, Mary L. Kopka, Richard E. Dickerson, David S. Goodsell:
  Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method. 539-546
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• Elsa F. Henriques, Maria João Ramos, Christopher A. Reynolds:
  Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein. 547-556
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• Andrew R. Poirrette, Peter J. Artymiuk, David W. Rice, Peter Willett:
  Comparison of protein surfaces using a genetic algorithm. 557-569
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• Ross D. King, Ashwin Srinivasan:
  The discovery of indicator variables for QSAR using inductive logic programming. 571-580
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• Peter W. Swaan, Francis C. Szoka Jr., Svein Øie:
  Molecular modeling of the intestinal bile acid carrier: A comparative molecular field analysis study. 581-588
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• María L. López-Rodríguez, María José Morcillo, Bellinda Benhamú, María Luisa Rosado:
  Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites. 589-599
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• Anders Berglund, Maria Cristina De Rosa, Svante Wold:
  Alignment of flexible molecules at their receptor site using 3D descriptors and Hi-PCA. 601-612
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