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ORCIDJournal of Computer-Aided Molecular Design, Volume 17
Volume 17, Number 1, January 2003
- Joachim A. Paier
, Thomas Stockner, Andreas Steinreiber, Kurt Faber, Walter M. F. Fabian:
Enantioselectivity of epoxide hydrolase catalysed oxirane ring opening: a 3D QSAR Study. 1-11
- Andreas Krämer, Hans W. Horn, Julia E. Rice:
Fast 3D molecular superposition and similarity search in databases of flexible molecules. 13-38 - Fabrizio Giordanetto, Paola Fossa, Giulia Menozzi, Silvia Schenone, Francesco Bondavalli, Angelo Ranise, Luisa Mosti:
Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study. 39-51 - Fabrizio Giordanetto, Paola Fossa, Giulia Menozzi, Luisa Mosti:
In silico rationalization of the structural and physicochemical requirements for photobiological activity in angelicine derivatives and their heteroanalogues. 53-64 - Philippa R. N. Wolohan, Robert D. Clark:
Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA. 65-76
Volume 17, Number 2-4, February 2003
- Terry R. Stouch, James R. Kenyon, Stephen R. Johnson, Xue-Qing Chen, Arthur M. Doweyko, Yi Li:
In silico ADME/Tox: why models fail. 83-92 - Philip J. Hajduk, Renaldo Mendoza, Andrew M. Petros, Jeffrey R. Huth, Mark G. Bures, Stephen W. Fesik, Yvonne C. Martin:
Ligand binding to domain-3 of human serum albumin: a chemometric analysis. 93-102 - L. Mark Hall, Lowell H. Hall, Lemont B. Kier:
QSAR modeling of beta-lactam binding to human serum proteins. 103-118 - John C. Dearden:
In silico prediction of drug toxicity. 119-127 - Paul J. Lewi, Marc R. de Jonge, Frederik F. D. Daeyaert, Lucien M. H. Koymans, H. Maarten Vinkers, Jan Heeres, Paul A. J. Janssen, Eddy Arnold, Kalyan Das, Art D. Clark Jr., Stephen H. Hughes, Paul L. Boyer, Marie-Pierre de Béthune, Rudi Pauwels, Koen Andries, Mike Kukla, Donald Ludovici, Bart De Corte, Robert Kavash, Chih Ho:
On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data. 129-134 - Robert E. Hormann, Laurence Dinan, Pensri Whiting:
Superimposition evaluation of ecdysteroid agonist chemotypes through multidimensional QSAR. 135-153 - Su J. Patankar, Peter C. Jurs:
Classification of HIV protease inhibitors on the basis of their antiviral potency using radial basis function neural networks. 155-171 - Tamas Kortvelyesi, Michael Silberstein, Sheldon Dennis, Sandor Vajda:
Improved mapping of protein binding sites. 173-186 - Alka Kurup:
C-QSAR: a database of 18, 000 QSARs and associated biological and physical data. 187-196 - Alka Kurup:
The nature of topological parameters. I. Are topological parameters 'fundamental properties'? 197-209 - Marvin Charton, Barbara Charton:
The nature of topological parameters. II. The composition of topological parameters. 211-221 - Andrew J. Holder, David M. Yourtee, Derek A. White, Alan G. Glaros, Robert Smith:
Chain melting temperature estimation for phosphatidyl cholines by quantum mechanically derived quantitative structure property relationships. 223-230 - Curt M. Breneman, C. Matthew Sundling, Nagamani Sukumar, Lingling Shen, William P. Katt, Mark J. Embrechts:
New developments in PEST shape/property hybrid descriptors. 231-240 - Alexander Golbraikh, Min Shen, Zhiyan Xiao, Yun-De Xiao, Kuo-Hsiung Lee, Alexander Tropsha:
Rational selection of training and test sets for the development of validated QSAR models. 241-253 - Walter Cedeño, Dimitris K. Agrafiotis:
Using particle swarms for the development of QSAR models based on K-nearest neighbor and kernel regression. 255-263 - Robert D. Clark:
Boosted leave-many-out cross-validation: the effect of training and test set diversity on PLS statistics. 265-275
Volume 17, Number 5-6, May-June 2003
- Irwin Rose de Alencar Menezes, Julio Cesar Dias Lopes, Carlos Alberto Montanari, Glaucius Oliva, Fernando Pavão, Marcelo Santos Castilho, Paulo C. Vieira, Mônica Tallarico Pupo:
3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi. 277-290 - Gilles Klopman, Hao Zhu, Gerhard F. Ecker, Peter Chiba:
MCASE study of the multidrug resistance reversal activity of propafenone analogs. 291-297 - Jan Kmunícek, Michal Bohác, Santos Luengo, Federico Gago, Rebecca C. Wade, Jirí Damborský:
Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. 299-311 - Peter Wolohan, David E. Reichert:
CoMFA and docking study of novel estrogen receptor subtype selective ligands. 313-328 - Shun-ichi Kawahara, Tadafumi Uchimaru, Kazunari Taira:
2-Pyridone and 3-oxo-1, 2, 6-thiadiazine-1, 1-dioxide derivatives: a new class of hydrogen bond equivalents of uracil. 329-334 - Paolo Mazzatorta, Marjan Vracko, Emilio Benfenati:
ANVAS: Artificial Neural Variables Adaptation System for descriptor selection. 335-346 - Nikolaus Stiefl, Gerhard Bringmann, Christian Rummey, Knut Baumann:
Evaluation of extended parameter sets for the 3D-QSAR technique MaP: Implications for interpretability and model quality exemplified by antimalarially active naphthylisoquinoline alkaloids. 347-365 - Aina Westrheim Ravna, Ingebrigt Sylte, Svein G. Dahl:
Molecular model of the neural dopamine transporter. 367-382 - Anne Techau Jørgensen, Morten Dahl Sørensen, Fredrik Björkling, Tommy Liljefors:
Binding of Alpha-hydroxy-beta-amino acid inhibitors to methionine aminopeptidase. The performance of two types of scoring functions. 383-397 - Hugo Kubinyi:
Book Review: Andrew R. Leach and Valerie J. Gillet. An Introduction to Chemoinformatics. 399
Volume 17, Number 7, July 2003
- Matthew D. Kelly, Ricardo L. Mancera:
A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein. 401-414 - Michael C. Hutter:
Prediction of blood-brain barrier permeation using quantum chemically derived information. 415-443 - Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson:
A Bayesian molecular interaction library. 435-461 - Pedro Alexandrino Fernandes, Alexandra T. P. Carvalho, A. T. Marques, A. L. F. Pereira, A. P. S. Madeira, Ana Sofia P. Ribeiro, A. F. R. Carvalho, E. T. A. Ricardo, F. J. V. Pinto, H. A. Santos, H. D. G. Mangericão, H. M. Martins, H. D. B. Pinto, Hugo R. R. Santos, Irina S. Moreira, M. J. V. Azeredo, R. P. S. Abreu, R. M. S. Oliveira, Sergio F. Sousa, R. J. A. M. Silva, Z. S. Mourão, Maria João Ramos:
New designs for MRI contrast agents. 463-473
Volume 17, Number 8, August 2003
- Haregewein Assefa, Shantaram Kamath, John K. Buolamwini:
3D-QSAR and docking studies on 4-anilinoquinazoline and 4-anilinoquinoline epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors. 475-493 - Jing Wang, Shek Ling Chan, Kal Ramnarayan:
Structure-based prediction of free energy changes of binding of PTP1B inhibitors. 495-513 - María L. López-Rodríguez, Bellinda Benhamú, Marta Murcia, Elsa Álvaro, Mercedes Campillo, Leonardo Pardo:
Benzimidazole derivatives. 4. The recognition of the voluminous substituent attached to the basic amino group of 5-HT4 receptor antagonists. 515-524 - Robin J. Rosenfeld, David S. Goodsell, Rabi A. Musah, Garrett M. Morris, David B. Goodin, Arthur J. Olson:
Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. 525-536 - Anne-Marie Harrison, Darren R. South, Peter Willett, Peter J. Artymiuk:
Representation, searching and discovery of patterns of bases in complex RNA structures. 537-549
Volume 17, Number 9, September 2003
- Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington, David van der Spoel:
Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10. 551-565 - H. Maarten Vinkers, Marc R. de Jonge, Frederik F. D. Daeyaert, Jan Heeres, Lucien M. H. Koymans, Joop H. van Lenthe, Paul J. Lewi, Henk Timmerman, Paul A. J. Janssen:
Inhibition and substrate recognition - a computational approach applied to HIV protease. 567-581 - César Portela, Carlos M. M. Afonso, Madalena M. M. Pinto, Maria João Ramos:
Computational studies of new potential antimalarial compounds - Stereoelectronic complementarity with the receptor. 583-595 - Andrey E. Muryshev, D. N. Tarasov, A. V. Butygin, O. Yu. Butygina, A. B. Aleksandrov, S. M. Nikitin:
A novel scoring function for molecular docking. 597-605 - Biye Ren:
New atom-type-based AI topological indices: Application to QSPR studies of aldehydes and ketones. 607-619
Volume 17, Number 10, October 2003
- Eric Pellegrini, Martin J. Field:
Development and testing of a de novo drug-design algorithm. 621-641 - Govindan Subramanian, Douglas B. Kitchen:
Computational models to predict blood-brain barrier permeation and CNS activity. 643-664 - Maykel Pérez González, Aliuska Morales Helguera:
TOPS-MODE versus DRAGON descriptors to predict permeability coefficients through low-density polyethylene. 665-672 - Alessandra Villa, Ronen Zangi, Gilles Pieffet, Alan E. Mark:
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin. 673-686 - Uli Fechner, Lutz Franke, Steffen Renner, Petra Schneider, Gisbert Schneider:
Comparison of correlation vector methods for ligand-based similarity searching. 687-698 - Adam Jarmula, Piotr Cieplak, Andrzej Les, Wojciech Rode:
Relative free energies of binding to thymidylate synthase of 2- and/or 4-thio and/or 5-fluoro analogues of dUMP. 699-710
Volume 17, Number 11, November 2003
- Javier de la Mata Mora, Camelia Muñoz-Caro, Alfonso Niño:
Thermodynamic conformational analysis and structural stability of the nicotinic analgesic ABT-594. 713-724 - Michal J. Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski:
Protein fragment reconstruction using various modeling techniques. 725-738 - Britta M. Bröer, Marion Gurrath, Hans-Dieter Höltje:
Molecular modelling studies on the ORL1-receptor and ORL1-agonists. 739-754 - Badry D. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III:
Comparative study of several algorithms for flexible ligand docking. 755-763 - Anders Poulsen, Berith Bjørnholm, Klaus Gundertofte, Irina D. Pogozheva, Tommy Liljefors:
Pharmacophore and receptor models for neurokinin receptors. 765-783 - Bernard Pirard:
Peroxisome Proliferator-Activated Receptors target family landscape: A chemometrical approach to ligand selectivity based on protein binding site analysis. 785-796
Volume 17, Number 12, December 2003
- Anu J. Tervo, Tommi H. Nyrönen, Toni Rönkkö, Antti Poso:
A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods. 797-810 - Ailan Cheng, Steven L. Dixon:
In silico models for the prediction of dose-dependent human hepatotoxicity. 811-823 - Vineet Pande, Rakesh K. Sharma, Jun-Ichiro Inoue, Masami Otsuka, Maria João Ramos:
A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) - DNA binding. 825-836 - Mattia Falconi, Gioia Altobelli, Maria Cristina Iovino, Vincenzo Politi, Alessandro Desideri:
Molecular dynamics simulation of Matrix Metalloproteinase 2: fluctuations and time evolution of recognition pockets. 837-848 - Berith F. Jensen, Morten Dahl Sørensen, Anne-Marie Kissmeyer, Fredrik Björkling, Kim Sonne, Søren Balling Engelsen, Lars Nørgaard:
Prediction of in vitro metabolic stability of calcitriol analogs by QSAR. 849-859 - Vincent Zoete, Olivier Michielin, Martin Karplus:
Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. 861-880
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