Journal of Computer-Aided Molecular Design, Volume 16

Volume 16, Number 1, January 2002

• Oleg A. Raevsky, Vladlen S. Skvortsov:
  3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling. 1-10
  
• Renxiao Wang, Luhua Lai, Shaomeng Wang:
  Further development and validation of empirical scoring functions for structure-based binding affinity prediction. 11-26
  
• Tingjun Hou, Wei Zhang, Xiaojie Xu:
  Molecular docking studies of a group of hydroxamate inhibitors with gelatinase-A by molecular dynamics. 27-41
  
• Richard M. Jackson:
  Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space. 43-57
  
• John W. Raymond, Peter Willett:
  Effectiveness of graph-based and fingerprint-based similarity measures for virtual screening of 2D chemical structure databases. 59-71
  

Volume 16, Number 2, February 2002

• Christian Th. Klein, Norbert Kaiblinger, Peter Wolschann:
  Internally defined distances in 3D-quantitative structure-activity relationships. 79-93
  
• Gabriel Vallejos, Marcos Caroli Rezende, Bruce K. Cassels:
  Charge-transfer interactions in the inhibition of MAO-A by phenylisopropylamines - a QSAR study. 95-103
  
• David J. Diller, Kenneth M. Merz Jr.:
  Can we separate active from inactive conformations? 105-112
  
• Oleksandr V. Buzko, Anthony C. Bishop, Kevan M. Shokat:
  Modified AutoDock for accurate docking of protein kinase inhibitors. 113-127
  
• Sally A. Hindle, Matthias Rarey, Christian Buning, Thomas Lengauer:
  Flexible docking under pharmacophore type constraints. 129-149
  

Volume 16, Number 3, March 2002

• Richard D. Taylor, Philip J. Jewsbury, Jonathan W. Essex:
  A review of protein-small molecule docking methods. 151-166
  
• Anne Techau Jørgensen, Per-Ola Norrby, Tommy Liljefors:
  Investigation of the metal binding site in methionine aminopeptidase by density functional theory. 167-179
  
• Mahindra T. Makhija, Vithal M. Kulkarni:
  3D-QSAR and molecular modeling of HIV-1 integrase inhibitors. 181-200
  
• Juswinder Singh, Herman van Vlijmen, Wen-Cherng Lee, Yusheng Liao, Ko-Chung Lin, Humayun Ateeq, Julio Cuervo, Craig Zimmerman, Charles Hammond, Michael Karpusas, Rex Palmer, Tapan Chattopadhyay, Steven P. Adams:
  3D QSAR (COMFA) of a series of potent and highly selective VLA-4 antagonists. 201-211
  
• Massimiliano Aschi, Danilo Roccatano, Alfredo Di Nola, Carlo Gallina, Enrico Gavuzzo, Giorgio Pochetti, Michael Pieper, Harald Tschesche, Fernando Mazza:
  Computational study of the catalytic domain of human neutrophil collagenase. Specific role of the S3 and S'3 subsites in the interaction with a phosphonate inhibitor. 213-225
  

Volume 16, Number 4, April 2002

• Antoine Logean, Didier Rognan:
  Recovery of known T-cell epitopes by computational scanning of a viral genome. 229-243
  
• Jonathan B. Baell, Andrew J. Harvey, Raymond S. Norton:
  Design and synthesis of type-III mimetics of ShK toxin. 245-262
  
• K. Senthilkumar, P. Kolandaivel:
  Quantum chemical studies on tautomerism of barbituric acid in gas phase and in solution. 263-272
  
• Anders Poulsen, Tommy Liljefors, Klaus Gundertofte, Berith Bjørnholm:
  A pharmacophore model for NK2 antagonist comprising compounds from several structurally diverse classes. 273-286
  
• Anderson Coser Gaudio, Carlos Alberto Montanari:
  HEPT derivatives as non-nucleoside inhibitors of HIV-1 reverse transcriptase: QSAR studies agree with the crystal structures. 287-295
  

Volume 16, Number 5-6, May - June 2002

• Chris L. Waller:
  Recent advances in molecular diversity. 299-300
  
• Mary P. Bradley:
  An overview of the diversity represented in commercially-available databases. 301-309
  
• Paul S. Charifson, W. Patrick Walters:
  Filtering databases and chemical libraries. 311-323
  
• Tudor I. Oprea:
  Current trends in lead discovery: Are we looking for the appropriate properties? 325-334
  
• Dimitris K. Agrafiotis:
  Multiobjective optimization of combinatorial libraries. 335-356
  
• Alexander Golbraikh, Alexander Tropsha:
  Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection. 357-369
  
• Valerie J. Gillet:
  Reactant- and product-based approaches to the design of combinatorial libraries. 371-380
  
• Sean Ekins, Bruno Boulanger, Peter W. Swaan, Maggie A. Z. Hupcey:
  Towards a new age of virtual ADME/TOX and multidimensional drug discovery. 381-401
  
• Scott Boyer, Ismael Zamora:
  New methods in predictive metabolism. 403-413
  
• Douglas A. Horton, Gregory T. Bourne, Mark L. Smythe:
  Exploring privileged structures: the combinatorial synthesis of cyclic peptides. 415-431
  
• Jürgen Bajorath:
  Chemoinformatics methods for systematic comparison of molecules from natural and synthetic sources and design of hybrid libraries. 431-439
  

Volume 16, Number 7, July 2002

• Lovisa Afzelius, Collen M. Masimirembwa, Anders Karlén, Tommy B. Andersson, Ismael Zamora:
  Discriminant and quantitative PLS analysis of competitive CYP2C9 inhibitors versus non-inhibitors using alignment independent GRIND descriptors. 443-458
  
• Martin Stahl, Nikolay P. Todorov, Timothy James, Harald Mauser, Hans-Joachim Böhm, Philip M. Dean:
  A validation study on the practical use of automated de novo design. 459-478
  
• Ricardo L. Mancera:
  De novo ligand design with explicit water molecules: an application to bacterial neuraminidase. 479-499
  
• F. De Rienzo, G. H. Grant, M. C. Menziani:
  Theoretical descriptors for the quantitative rationalisation of plastocyanin mutant functional propertiess. 501-509
  
• James J. Chambers, David E. Nichols:
  A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor. 511-520
  
• John W. Raymond, Peter Willett:
  Maximum common subgraph isomorphism algorithms for the matching of chemical structures. 521-533
  

Volume 16, Number 8-9, August - September 2002

• Irini A. Doytchinova, Darren R. Flower:
  A Comparative Molecular Similarity Index Analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. 535-544
  
• S. Sardana, A. K. Madan:
  Predicting anticonvulsant activity of benzamides/benzylamines: computational approach using topological descriptors. 545-550
  
• Stefan Kamphausen, Nils Höltge, Frank Wirsching, Corinna Morys-Wortmann, Daniel Riester, Ruediger Goetz, Marcel Thürk, Andreas Schwienhorst:
  Genetic algorithm for the design of molecules with desired properties. 551-567
  
• Albert Salichs, M. López, V. Segarra, Modesto Orozco, F. Javier Luque:
  Fast estimation of hydrogen-bonding donor and acceptor propensities: a GMIPp study. 569-583
  
• Andrea J. H. Reaka, Chris M. W. Ho, Garland R. Marshall:
  Metal complexes of chiral pentaazacrowns as conformational templates for beta-turn recognition. 585-600
  
• Hyunmyung Kim, Karpjoo Jeong, Sangsan Lee, Seunho Jung:
  Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A). 601-610
  
• Brian W. Clare:
  QSAR of benzene derivatives: comparison of classical descriptors, quantum theoretic parameters and flip regression, exemplified by phenylalkylamine hallucinogens. 611-633
  
• Laurent David, Patricia Amara, Martin J. Field, François Major:
  Parametrization of a force field for metals complexed to biomacromolecules: applications to Fe(II), Cu(II) and Pb(II). 635-651
  
• Yogendra Patel, Valerie J. Gillet, Gianpaolo Bravi, Andrew R. Leach:
  A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP. 653-681
  

Volume 16, Number 10, October 2002

• R. Pouplana, Juan J. Lozano, C. Pérez, J. Ruiz:
  Structure-based QSAR study on differential inhibition of human prostaglandin endoperoxide H synthase-2 (COX-2) by nonsteroidal anti-inflammatory drugs. 683-709
  
• Lennart Eriksson, Erik Johansson, Fredrik Lindgren, Michael Sjöström, Svante Wold:
  Megavariate analysis of hierarchical QSAR data. 711-726
  
• Richard D. Beger, Dan A. Buzatu, Jon G. Wilkes:
  Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR. 727-740
  
• Christopher W. Murray, Marcel L. Verdonk:
  The consequences of translational and rotational entropy lost by small molecules on binding to proteins. 741-753
  
• P.-L. Chau, P. W. A. Howe:
  Analysis methods for identifying coordinated movements during ligand unbinding. 755-765
  

Volume 16, Number 11, November 2002

• Ferran Sanz, Federico Gago:
  Current perspective of information technologies in drug discovery. 767-768
  
• Antonio Carrieri, Andrea Carotti, M. Letizia Barreca, Cosimo Altomare:
  Binding models of reversible inhibitors to type-B monoamine oxidase. 769-778
  
• Gabriele Costantino, Antonio Macchiarulo, Maxim Belenikin, Roberto Pellicciari:
  Molecular dynamics simulation of the ligand binding domain of mGluR1 in response to agonist and antagonist binding. 779-784
  
• Christian Th. Klein, Dominik Kaiser, Stephan Kopp, Peter Chiba, Gerhard F. Ecker:
  Similarity based SAR (SIBAR) as tool for early ADME profiling. 785-793
  
• Kirstin Jöhren, Hans-Dieter Höltje:
  A model of the human M₂ muscarinic acetylcholine receptor. 795-801
  
• Stanley A. Lang, Andrey V. Kozyukov, Konstantin V. Balakin, Andrey V. Skorenko, Andrey A. Ivashchenko, Nikolay P. Savchuk:
  Classification scheme for the design of serine protease targeted compound libraries. 803-807
  
• Manuel Pastor, Paolo Benedetti, Angelo Carotti, Antonio Carrieri, Carlos Díaz, Cristina Herráiz, Hans-Dieter Höltje, M. Isabel Loza, Tudor I. Oprea, Fernando Padín, Francesc Pubill, Ferran Sanz, Friederike Stoll:
  Distant collaboration in drug discovery: The LINK3D project. 809-818
  
• Vladimir Poroikov, Dmitrii Filimonov:
  How to acquire new biological activities in old compounds by computer prediction. 819-824
  
• Wolfgang Sippl:
  Development of biologically active compounds by combining 3D QSAR and structure-based design methods. 825-830
  
• Kristin Tøndel, Endre Anderssen, Finn Drabløs:
  Protein Alpha Shape Similarity Analysis (PASSA): A new method for mapping protein binding sites. Application in the design of a selective inhibitor of Tyrosine kinase 2. 831-840
  
• Ernest L. Mehler, X. Periole, S. A. Hassan, Harel Weinstein:
  Key issues in the computational simulation of GPCR function: representation of loop domains. 841-853
  

Volume 16, Number 12, December 2002

• Louise Birch, Christopher W. Murray, Michael J. Hartshorn, Ian J. Tickle, Marcel L. Verdonk:
  Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. 855-869
  
• Michael J. Hartshorn:
  AstexViewerTM: a visualisation aid for structure-based drug design. 871-881
  
• Maria I. Zavodszky, Paul C. Sanschagrin, Rajesh S. Korde, Leslie A. Kuhn:
  Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. 883-902
  
• Alexander Weber, Andreas Teckentrup, Hans Briem:
  Flexsim-R: A virtual affinity fingerprint descriptor to calculate similarities of functional groups. 903-916
  
• Mariano Grasselli, Osvaldo Cascone, F. Birger Anspach, José María Delfino:
  On the molecular interaction between lactoferrin and the dye Red HE-3B. A novel approach for docking a charged and highly flexible molecule to protein surfaces. 917-934
  
• Gabriela Iurcu Mustata, James M. Briggs:
  A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase. 935-953
  

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