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ORCIDJournal of Computer-Aided Molecular Design, Volume 18
Volume 18, Number 1, January 2004
- Dilek Duran, Viktorya Aviyente
, Canan Baysal:
Theoretical study of selective methylation in the synthesis of azithromycin. 1-11 - Marta Pinto, Juan Jesús Pérez, Jaime Rubio-Martinez:
Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-xL and Bcl-2 proteins. 13-22 - Doron Chema, Doron Eren, Avner Yayon, Amiram Goldblum, Andrea Zaliani:
Identifying the binding mode of a molecular scaffold. 23-40 - Marcin Król, Tomasz Borowski, Irena Roterman, Barbara Piekarska, Barbara Stopa, Joanna Rybarska, Leszek Konieczny:
Force-field parametrization and molecular dynamics simulations of Congo red. 41-53 - Keith Mason, Nehal M. Patel, Aric Ledel, Ciamac Cyrus Moallemi, Edward A. Wintner:
Mapping protein pockets through their potential small-molecule binding volumes: QSCD applied to biological protein structures. 55-70
Volume 18, Number 2, February 2004
- Aixia Yan, Johann Gasteiger, Michael Krug, Soheila Anzali:
Linear and nonlinear functions on modeling of aqueous solubility of organic compounds by two structure representation methods. 75-87 - David G. Lloyd, Alfonso T. García-Sosa, Ian L. Alberts, Nikolay P. Todorov, Ricardo L. Mancera:
The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models. 89-100 - Kun Wang, Marta Murcia, Pere Constans, Carlos Pérez, Angel R. Ortiz:
Gaussian mapping of chemical fragments in ligand binding sites. 101-118 - Stefanie Bendels, Hans-Dieter Höltje:
Comparison of a 3D-model of the classical Alpha-scorpion toxin V from Leiurus quinquestriatus quinquestriatus with other scorpion toxins. 119-133 - Paul J. Smith, Paul L. A. Popelier:
Quantitative structure-activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives. 135-143 - Dilek Duran, Viktorya Aviyente, Canan Baysal:
Solvent effect on the synthesis of clarithromycin: A molecular dynamics study. 145-154
Volume 18, Number 3, March 2004
- Patrizia Crivori, Ismael Zamora, Bill Speed, Christian Orrenius, Italo Poggesi:
Model based on GRID-derived descriptors for estimating CYP3A4 enzyme stability of potential drug candidates. 155-166 - Alessandro Pedretti, Luigi Villa, Giulio Vistoli:
VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. 167-173 - Kari Tuppurainen, Marja Viisas, Mikael Peräkylä, Reino Laatikainen:
Ligand intramolecular motions in ligand-protein interaction: ALPHA, a novel dynamic descriptor and a QSAR study with extended steroid benchmark dataset. 175-187 - S. David Morley, Mohammad Afshar:
Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock. 189-208 - Silvina C. Pellegrinet, María A. Silva, Jonathan M. Goodman:
A promising enantioselective Diels-Alder dienophile by computer-assisted rational design: 2, 5-diphenyl-1-vinyl-borolane. 209-214 - Marjan A. Rafiee, Nasser L. Hadipour, Hossein Naderi-manesh:
A correlation study of quinoline derivatives and their pharmaceutical behavior by ab initio calculated NQR parameters. 215-220
Volume 18, Number 4, April 2004
- Thomas J. Oldfield:
A Java applet for multiple linked visualization of protein structure and sequence. 225-234 - Ami Yi-Ching Yang, Per Källblad, Ricardo L. Mancera:
Molecular modelling prediction of ligand binding site flexibility. 235-250 - Y. H. Yu, Benzhuo Lu, J. G. Han, P. F. Zhang:
Scoring protein-protein docked structures based on the balance and tightness of binding. 251-260 - Vladimir D. Ozrin, M. V. Subbotin, S. M. Nikitin:
PLASS: Protein-ligand affinity statistical score - a knowledge-based force-field model of interaction derived from the PDB. 261-270 - Silvia N. Crivelli, Oliver Kreylos, Bernd Hamann, Nelson L. Max, Wes Bethel:
ProteinShop: A tool for interactive protein manipulation and steering. 271-285 - Lars Olsen, Ingrid Pettersson, Lars Hemmingsen, Hans-Werner Adolph, Flemming Steen Jørgensen:
Docking and scoring of metallo-β-lactamases inhibitors. 287-302
Volume 18, Number 5, May 2004
- D. Joseph Harriman, Ghislain Deslongchamps:
Reverse-docking as a computational tool for the study of asymmetric organocatalysis. 303-308 - Jeffrey J. Sutherland, Donald F. Weaver:
Three-dimensional quantitative structure-activity and structure-selectivity relationships of dihydrofolate reductase inhibitors. 309-331 - Li Xing, Edward Hodgkin, Qian Liu, David Sedlock:
Evaluation and application of multiple scoring functions for a virtual screening experiment. 333-344 - José L. Medina-Franco, Sergio Rodríguez-Morales, Cecilia Juárez-Gordiano, Alicia Hernández-Campos, Rafael Castillo:
Docking-based CoMFA and CoMSIA studies of non-nucleoside reverse transcriptase inhibitors of the pyridinone derivative type. 345-360 - Paola Cratteri, Maria Novella Romanelli, Gabriele Cruciani, Claudia Bonaccini, Fabrizio Melani:
GRIND-derived pharmacophore model for a series of α-tropanyl derivative ligands of the sigma-2 receptor*. 361-374
Volume 18, Number 6, June 2004
- Hwangseo Park, Sangyoub Lee:
Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors. 375-388 - Huanxiang Liu, Ruisheng Zhang, Xiaojun Yao, Mancang Liu, Zhide Hu, Bo Tao Fan:
QSAR and classification models of a novel series of COX-2 selective inhibitors: 1, 5-diarylimidazoles based on support vector machines. 389-399 - Jukka V. Lehtonen, Dan-Johan Still, Ville-Veikko Rantanen, Jan Ekholm, Dag Björklund, Zuhair Iftikhar, Mikko Huhtala, Susanna Repo, Antti Jussila, Jussi Jaakkola, Olli T. Pentikäinen, Tommi H. Nyrönen, Tiina Salminen, Mats Gyllenberg, Mark S. Johnson:
BODIL: a molecular modeling environment for structure-function analysis and drug design. 401-419 - Jóhannes Reynisson, Edward McDonald:
Tuning of hydrogen bond strength using substituents on phenol and aniline: A possible ligand design strategy. 421-431 - John Mongan:
Interactive essential dynamics. 433-436
Volume 18, Number 7, July 2004
- Marius Olah, Cristian Bologa, Tudor I. Oprea:
An automated PLS search for biologically relevant QSAR descriptors. 437-449 - Anthony Nicholls, Norah E. MacCuish, John MacCuish:
Variable selection and model validation of 2D and 3D molecular descriptors>. 451-474 - Pierre-Jean L'Heureux, Julie Carreau, Yoshua Bengio, Olivier Delalleau, Shi Yi Yue:
Locally Linear Embedding for dimensionality reduction in QSAR. 475-482 - Ersin Bayram, Peter Santago II, Rebecca Harris, Yun-De Xiao, Aaron Clauset, Jeffrey D. Schmitt:
Genetic algorithms and self-organizing maps: a powerful combination for modeling complex QSAR and QSPR problems. 483-493 - David W. Salt, Laura Maccari, Maurizio Botta, Martyn G. Ford:
Variable selection and specification of robust QSAR models from multicollinear data: arylpiperazinyl derivatives with affinity and selectivity for α2-adrenoceptors. 495-509 - Sabine Schefzick, Mary P. Bradley:
Comparison of commercially available genetic algorithms: GAs as variable selection tool. 511-521 - Andrew C. Good, Sung-Jin Cho, Jonathan S. Mason:
Descriptors you can count on? Normalized and filtered pharmacophore descriptors for virtual screening. 523-527 - Andrew C. Good, Mark A. Hermsmeier, Sally A. Hindle:
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments. 529-536 - John H. Kalivas, Joel B. Forrester, Heather A. Seipel:
QSAR modeling based on the bias/variance compromise: a harmonious. 537-547 - Knut Baumann, Nikolaus Stiefl:
Validation tools for variable subset regression. 549-562 - Robert D. Clark, Peter C. Fox:
Statistical variation in progressive scrambling. 563-576 - Nadège Piclin, Marco Pintore, Christophe Wechman, Jacques R. Chrétien:
Classification of a large anticancer data set by Adaptive Fuzzy Partition. 577-586 - Arthur M. Doweyko:
3D-QSAR illusions. 587-596
Volume 18, Number 10, October 2004
- Michael R. Ziebell, Glenn D. Prestwich:
Interactions of peptide mimics of hyaluronic acid with the receptor for hyaluronan mediated motility (RHAMM). 597-614 - Yovani Marrero-Ponce, Juan A. Castillo-Garit, Ervelio Olazabal, Hector S. Serrano, Alcidez Morales, Nilo Castañedo, Froylán Ibarra-Velarde, Alma Huesca-Guillen, Elisa Jorge, Arletys del Valle, Francisco Torrens, Eduardo A. Castro:
Tomocomd-Cardd, a novel approach for computer-aided ' rational' drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds. 615-634 - Xavier Fradera, Jasmit Kaur, Jordi Mestres:
Unsupervised guided docking of covalently bound ligands. 635-650 - Gábor Maksay, Miklós Simonyi, Zsolt Bikádi:
Subunit rotation models activation of serotonin 5-HT3AB receptors by agonists. 651-664
Volume 18, Number 11, November 2004
- Simon J. Cottrell, Valerie J. Gillet, Robin Taylor, David J. Wilton:
Generation of multiple pharmacophore hypotheses using multiobjective optimisation techniques. 665-682 - Giuseppe Ermondi, Giulia Caron, Raelene Lawrence, Dario Longo:
Docking studies on NSAID/COX-2 isozyme complexes using Contact Statistics analysis. 683-696 - Katrin Kupas, Alfred Ultsch, Gerhard Klebe:
Comparison of substructural epitopes in enzyme active sites using self-organizing maps. 697-708 - Paul L. A. Popelier, Paul J. Smith, Usman A. Chaudry:
Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives. 709-718 - Kathleen M. Gilbert, William J. Skawinski, Milind Misra, Kristina A. Paris, Neelam Naik, Ronald A. Buono, Howard M. Deutsch, Carol A. Venanzi:
Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods. 719-738
Volume 18, Number 12, December 2004
- Rajeshri G. Karki, Yun Tang, Terrence R. Burke Jr., Marc C. Nicklaus:
Model of full-length HIV-1 integrase complexed with viral DNA as template for anti-HIV drug design. 739-760 - Nathan Brown, Ben McKay, Johann Gasteiger:
The de novo design of median molecules within a property range of interest. 761-771 - Alessandro Curioni, Tiziana Mordasini, Wanda Andreoni:
Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields. 773-784 - Viktor Kettmann, Daniela Kostálová, Hans-Dieter Höltje:
Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model. 785-796 - Guang-Zheng Zhang, De-Shuang Huang:
Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. 797-810
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