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    Journal: Journal of Computer-Aided Molecular Design

    Volume 12, Issue 6

    525 -- 537Ian 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
    539 -- 546Wynn 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
    547 -- 556Elsa F. Henriques, Maria João Ramos, Christopher A. Reynolds. Inclusion of conserved buried water molecules in the model structure of rat submaxillary kallikrein
    557 -- 569Andrew R. Poirrette, Peter J. Artymiuk, David W. Rice, Peter Willett 0002. Comparison of protein surfaces using a genetic algorithm
    571 -- 580Ross D. King, Ashwin Srinivasan. The discovery of indicator variables for QSAR using inductive logic programming
    581 -- 588Peter W. Swaan, Francis C. Szoka Jr., Svein Øie. Molecular modeling of the intestinal bile acid carrier: A comparative molecular field analysis study
    589 -- 599María L. López-Rodríguez, María José Morcillo, Bellinda Benhamú, María Luisa Rosado. Comparative receptor mapping of serotoninergic 5-HT3 and 5-HT4 binding sites
    601 -- 612Anders Berglund, Maria Cristina De Rosa, Svante Wold. Alignment of flexible molecules at their receptor site using 3D descriptors and Hi-PCA

    Volume 12, Issue 5

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

    Volume 12, Issue 4

    309 -- 323Hans-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
    325 -- 333Andrey A. Bliznyuk, Jill E. Gready. Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase
    335 -- 349Nikolay P. Todorov, Philip M. Dean. A branch-and-bound method for optimal atom-type assignment in de novo ligand design
    351 -- 360M. 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
    361 -- 372Paola Fossa, Raffaella Boggia, Luisa Mosti. Toward the identification of the cardiac cGMP inhibited-phosphodiesterase catalytic site
    373 -- 382Divi Venkateswarlu, Jerzy Leszczynski. Tautomeric equilibria in 8-oxopurines: Implications for mutagenicity
    383 -- 396Jonas Boström, Per-Ola Norrby, Tommy Liljefors. Conformational energy penalties of protein-bound ligands
    397 -- 409Somsak 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

    Volume 12, Issue 3

    215 -- 227Randall 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
    229 -- 240Anton V. Filikov, Thomas L. James. Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein
    241 -- 257Fabio Zuccotto, Andrew C. R. Martin, Roman A. Laskowski, Janet M. Thornton, Ian H. Gilbert. Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania
    259 -- 273Carlos 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
    275 -- 287Cezary Czaplewski, Rajmund Kazmierkiewicz, Jerzy Ciarkowski. Molecular modeling of the human vasopressin V2 receptor/agonist complex
    289 -- 299André H. Juffer, Hans J. Vogel. A flexible triangulation method to describe the solvent-accessible surface of biopolymers
    301 -- 307Martti Ovaska, Ari Yliniemelä. A semiempirical study on inhibition of catechol O-methyltransferase by substituted catechols

    Volume 12, Issue 2

    99 -- 110Roy 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
    111 -- 118Marta Filizola, Juan J. Perez, Maria Cartenì-Farina. BUNDLE: A program for building the transmembrane domains of G-protein-coupled receptors
    119 -- 131John 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
    133 -- 146Traian Sulea, Ludovic Kurunczi, Tudor I. Oprea, Zeno Simon. MTD-ADJ: A multiconformational minimal topologic difference for determining bioactive conformers using adjusted biological activities
    147 -- 163Samuel Petit, Frédéric Brard, Gérard Coquerel, Guy Perez, François Tron. Structural models of antibody variable fragments: A method for investigating binding mechanisms
    165 -- 181John 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
    183 -- 193Marcel 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
    195 -- 213Louis Carlacci. Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

    Volume 12, Issue 1

    1 -- 6Gerhard Müller, Henry Giera. Protein secondary structure templates derived from bioactive natural products - Combinatorial chemistry meets structure-based design
    7 -- 14Nuria B. Centeno, Juan J. Perez. A proposed bioactive conformation of Peptide T
    15 -- 25Anderson 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
    27 -- 35Tomas Hansson, John Marelius, Johan Åqvist. Ligand binding affinity prediction by linear interaction energy methods
    37 -- 51Paul R. Gerber. Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field MAB
    53 -- 61Mischa L. M. Beckers, Willem J. Melssen, Lutgarde M. C. Buydens. Predicting nucleic acid torsion angle values using artificial neural networks
    63 -- 79Sanja Tomic, Razif R. Gabdoulline, Biserka Kojic-Prodic, Rebecca C. Wade. Classification of auxin plant hormones by interaction property similarity indices
    81 -- 93Jonas 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
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