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ORCIDJournal of Computer-Aided Molecular Design, Volume 14
Volume 14, Number 1, January 2000
- David B. Turner
, Peter Willett:
Evaluation of the EVA descriptor for QSAR studies: 3. The use of a genetic algorithm to search for models with enhanced predictive properties (EVA_GA). 1-21 - Ryan T. Koehler, Hugo O. Villar:
Statistical relationships among docking scores for different protein binding sites. 23-37 - Jordi Mestres, Douglas C. Rohrer, Gerald M. Maggiora:
A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching. 39-51 - Didier Rognan, Anette Stryhn, Lars Fugger, Stig Lyngbæk, Jan Engberg, Peter Sejer Andersen, Søren Buus:
Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. I. Recognition by two alpha-beta T cell receptors. 53-69 - Didier Rognan, Jan Engberg, Anette Stryhn, Peter Sejer Andersen, Søren Buus:
Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. II. Cross-reaction between a monoclonal antibody and two alpha-beta T cell receptors. 71-82 - Patrick Aloy, José M. Mas, Marc A. Martí-Renom, Enrique Querol, Francesc X. Avilés, Baldomero Oliva:
Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2. 83-92 - Francesca De Rienzo, Francesca Fanelli, Maria Cristina Menziani, Pier Giuseppe De Benedetti:
Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4. 93-116
Volume 14, Number 2, February 2000
- G. Schaftenaar, Jan H. Noordik:
Molden: a pre- and post-processing program for molecular and electronic structures. 123-134 - Mark Froimowitz, Kuo-Ming Wu, Jason Rodrigo, Clifford George:
Conformational preferences of the potent dopamine reuptake blocker BTCP and its analogs and their incorporation into a pharmacophore model. 135-146 - Raquel García-Nieto, Carlos Pérez, Federico Gago:
Automated docking and molecular dynamics simulations of nimesulide in the cyclooxygenase active site of human prostaglandin-endoperoxide synthase-2 (COX-2). 147-160 - Amedeo Caflisch, Hans J. Schramm, Martin Karplus:
Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach. 161-179 - Mehran Jalaie, Jon A. Erickson:
Homology model directed alignment selection for comparative molecular field analysis: Application to photosystem II inhibitors. 181-197 - Ajay N. Jain:
Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition. 199-213
Volume 14, Number 3, April 2000
- Christian Lemmen, Thomas Lengauer:
Computational methods for the structural alignment of molecules. 215-232 - G. Schaftenaar, Jan H. Noordik:
The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges. 233-242 - Hülya Yekeler:
Ab initio study on tautomerism of 2-thiouracil in the gas phase and in solution. 243-250 - Tudor I. Oprea:
Property distribution of drug-related chemical databases. 251-264 - Keigo Gohda, Ichiro Mori, Daisaku Ohta, Takeshi Kikuchi:
A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method. 265-275 - Enrica Filipponi, Violetta Cecchetti, Oriana Tabarrini, Daniela Bonelli, Arnaldo Fravolini:
Chemometric rationalization of the structural and physicochemical basis for selective cyclooxygenase-2 inhibition: Toward more specific ligands. 277-291 - Emanuela Gancia, Gianpaolo Bravi, Paolo Mascagni, Andrea Zaliani:
Global 3D-QSAR methods: MS-WHIM and autocorrelation. 293-306
Volume 14, Number 4, May 2000
- Jian Hui Wu, Christopher A. Reynolds:
Cyclophosphamides as hypoxia-activated diffusible cytotoxins: A theoretical study. 307-316 - Hervé Minoux, Christophe Chipot, David Brown, Bernard Maigret:
Structural analysis of the KGD sequence loop of barbourin, an alpha-IIb-beta-3-specific disintegrin. 317-327 - Begoña Hernández, F. Javier Luque, Modesto Orozco:
Mixed QM/MM molecular electrostatic potentials. 329-339 - Juan José Lozano, Manuel Pastor, Gabriele Cruciani, Katrin Gaedt, Nuria B. Centeno, Federico Gago, Ferran Sanz:
3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands. 341-353 - Fabrizio Manetti, Federico Corelli, Nicola Mongelli, Andrea Lombardi Borgia, Maurizio Botta:
Research on anti-HIV-1 agents. Investigation on the CD4-Suradista binding mode through docking experiments. 355-368 - Louis Carlacci:
Conformational analysis of a farnesyltransferase peptide inhibitor, CVIM. 369-382 - G. Patrick Brady Jr., Pieter F. W. Stouten:
Fast prediction and visualization of protein binding pockets with PASS. 383-401
Volume 14, Number 5, July 2000
- Pascal Furet, Juerg Zimmermann, Hans-Georg Capraro, Thomas Meyer, Patricia Imbach:
Structure-based design of potent CDK1 inhibitors derived from olomoucine. 403-409 - Thomas Fox, Eric E. J. Haaksma:
Computer based screening of compound databases: 1. Preselection of benzamidine-based thrombin inhibitors. 411-425 - Klaus-Jürgen Schleifer, E. Tot:
Pharmacophore modelling of structurally unusual diltiazem mimics at L-type calcium channels. 427-433 - Sookhee Ha, Romana Andreani, Arthur Robbins, Ingo Muegge:
Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors. 435-448 - Dominique Douguet, Etienne Thoreau, Gérard Grassy:
A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm. 449-466 - Klaus-Jürgen Schleifer:
Pseudoreceptor model for ryanodine derivatives at calcium release channels. 467-475 - Xavier Gironés, Lluís Amat, David Robert, Ramon Carbó-Dorca:
Use of electron-electron repulsion energy as a molecular descriptor in QSAR and QSPR studies. 477-485 - Gisbert Schneider, Man-Ling Lee, Martin Stahl, Petra Schneider:
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. 487-494 - Vijay M. Gokhale, Vithal M. Kulkarni:
Selectivity analysis of 5-(arylthio)-2, 4-diaminoquinazolines as inhibitors of Candida albicans dihydrofolate reductase by molecular dynamics simulations. 495-506
Volume 14, Number 6, August 2000
- Xavier Daura, Eric E. J. Haaksma, Wilfred F. van Gunsteren:
Factor Xa: Simulation studies with an eye to inhibitor design. 507-529 - J. Grembecka, W. Andrzej Sokalski, P. Kafarski:
Computer-aided design and activity prediction of leucine aminopeptidase inhibitors. 531-544 - Ulf Norinder:
Refinement of Catalyst hypotheses using simplex optimisation. 545-557 - Wolfgang Sippl:
Receptor-based 3D QSAR analysis of estrogen receptor ligands - merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods. 559-572 - David A. Cosgrove, Denis M. Bayada, A. Peter Johnson:
A novel method of aligning molecules by local surface shape similarity. 573-591 - Anton V. Filikov, Venkatraman Mohan, Timothy A. Vickers, Richard H. Griffey, P. Dan Cook, Ruben Abagyan, Thomas L. James:
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. 593-610
Volume 14, Number 7, October 2000
- Sandra Handschuh, Bernd Goldfuss, Jiangang Chen, Johann Gasteiger, Kendall N. Houk:
Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities. 611-629 - Robert Jäger, K. Friedemann Schmidt, Bernd Schilling, Jürgen Brickmann:
Localization and quantification of hydrophobicity: The molecular free energy density (MolFESD) concept and its application to sweetness recognition. 631-646 - Salvatore Guccione, Arthur M. Doweyko, Hongming Chen, Gloria Uccello Barretta, Federica Balzano:
3D-QSAR using 'Multiconformer' alignment: The use of HASL in the analysis of 5-HT1A thienopyrimidinone ligands. 647-657 - Roland G. Winkler, S. Fioravanti, G. Ciccotti, C. Margheritis, M. Villa:
Hydration of beta-cyclodextrin: A molecular dynamics simulation study. 659-667 - Takahiro Suzuki, Masaru Ishida, Walter M. F. Fabian:
Classical QSAR and comparative molecular field analyses of the host-guest interaction of organic molecules with cyclodextrins. 669-678 - Jorge Gálvez, Ramón García-Domenech, Carolina de Gregorio-Alapont:
Indices of differences of path lengths: Novel topological descriptors derived from electronic interferences in graphs. 679-687 - Haluk Resat, F. Aylin Sungur, Maciej Baginski, Edward Borowski, Viktorya Aviyente:
Conformational properties of amphotericin B amide derivatives - impact on selective toxicity. 689-703
Volume 14, Number 8, November 2000
- Carl D. Elkin, Harmon J. Zuccola, James M. Hogle, Diane Joseph-McCarthy:
Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization. 705-718 - Paul A. M. van Hooft, Hans-Dieter Höltje:
Construction of a full three-dimensional model of the transpeptidase domain of Streptococcus pneumoniae PBP2x starting from its C-alpha-atom coordinates. 719-730 - Gennady Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose:
Deciphering common failures in molecular docking of ligand-protein complexes. 731-751 - Nunzia Cinone, Hans-Dieter Höltje, Angelo Carotti:
Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands. 753-768 - Jonas Boström, Klaus Gundertofte, Tommy Liljefors:
A pharmacophore model for dopamine D4 receptor antagonists. 769-786 - J. Willem M. Nissink, Marcel L. Verdonk, Gerhard Klebe:
Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation. 787-803
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