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ORCIDJournal 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 - Francesca De Rienzo, Guy H. Grant, Maria Cristina 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
- Ramon Pouplana, Juan José 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 - Pak-Lee Chau, Peter William Arthur 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, María 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, Xavier 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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