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ORCIDJournal of Computer-Aided Molecular Design, Volume 19
Volume 19, Number 1, January 2005
- Philip S. Hammond, Yudong Wu, Rebecca Harris, Todd J. Minehardt, Roberto Car, Jeffrey D. Schmitt:
Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics. 1-15 - Hwangseo Park, Sangyoub Lee:
Free energy perturbation approach to the critical assessment of selective cyclooxygenase-2 inhibitors. 17-31 - Huanxiang Liu
, Rongjing Hu, Ruisheng Zhang, Xiaojun Yao, Mancang Liu, Zhide Hu, Bo Tao Fan:
The prediction of human oral absorption for diffusion rate-limited drugs based on heuristic method and support vector machine. 33-46 - Sergey Nikitin, Natalia Zaitseva, Olga Demina, Vera Solovieva, Evgeny Mazin, Sergey Mikhalev, Maxim Smolov, Anatoliy Rubinov, Peter Vlasov, Dmitry Lepikhin, Denis Khachko, Valery Fokin, Cary Queen, Viktor Zosimov:
A very large diversity space of synthetically accessible compounds for use with drug design programs. 47-63
Volume 19, Number 2, February 2005
- Deliang L. Chen, Glen E. Kellogg:
A computational tool to optimize ligand selectivity between two similar biomacromolecular targets. 69-82 - Carlos H. Tomich P. Silva, Ivone Carvalho, C. A. Taft:
Homology modeling and molecular interaction field studies of α-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors. 83-92 - Philip Prathipati, Anil K. Saxena:
Characterization of β3-adrenergic receptor: determination of pharmacophore and 3D QSAR model for β3 adrenergic receptor agonism. 93-110 - Karen A. Rossi, Jay A. Markwalder, Steven P. Seitz, Chong-Hwan Chang, Sarah Cox, Michael D. Boisclair, Leonardo Brizuela, Stephen L. Brenner, Pieter F. W. Stouten:
Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors. 111-122 - Adam Jarmula, Piotr Cieplak, William R. Montfort:
5, 10-Methylene-5, 6, 7, 8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies. 123-136
Volume 19, Number 3, March 2005
- Yong-Hua Wang, Yan Li, Sheng-Li Yang, Ling Yang:
An in silico approach for screening flavonoids as P-glycoprotein inhibitors based on a Bayesian-regularized neural network. 137-147 - Bernd Rupp, Stephan Raub, Christel M. Marian, Hans-Dieter Höltje:
Molecular design of two sterol 14α-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole. 149-163 - Hernán Alonso, Malcolm B. Gillies, Peter L. Cummins, Andrey A. Bliznyuk, Jill E. Gready:
Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase. 165-187 - Jan M. Kriegl, Thomas Arnhold, Bernd Beck, Thomas Fox:
A support vector machine approach to classify human cytochrome P450 3A4 inhibitors. 189-201 - Irini A. Doytchinova, Valerie Walshe, Persephone Borrow, Darren R. Flower:
Towards the chemometric dissection of peptide - HLA-A*0201 binding affinity: comparison of local and global QSAR models. 203-212
Volume 19, Number 4, April 2005
- Dakshanamurthy Sivanesan, Rajendram V. Rajnarayanan, Jason Doherty, Nagarajan Pattabiraman:
In-silico Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach. 213-228 - José L. Medina-Franco, Alexander Golbraikh, Scott Oloff, Rafael Castillo, Alexander Tropsha:
Quantitative Structure-activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the k Nearest Neighbor Method and QSAR-based Database Mining. 229-242 - Haifeng Chen, Bo Tao Fan, Chenyang Zhao, Lan Xie, Chun-Hong Zhao, Ting Zhou, Kuo-Hsiung Lee, Graham Allaway:
Computational Studies and Drug Design for HIV-1 Reverse Transcriptase Inhibitors of 3′, 4′-di-O-(S)-camphanoyl-(+)-cis-Khellactone (DCK) Analogs. 243-258 - Guido Angelini, Giorgio Cerichelli, Simona Cerritelli, Marco Pierini, Gabriella Siani, Claudio Villani:
An Effective Simulation of Aqueous Micellar Aggregates by Computational Models. 259-269 - Eszter Hazai, Zsolt Bikádi, Miklós Simonyi, David Kupfer:
Association of Cytochrome P450 Enzymes is a Determining Factor in their Catalytic Activity. 271-285
Volume 19, Number 5, May 2005
- Shantaram Kamath, John K. Buolamwini:
Asp746 to Glycine Change May have a Greater Influence than Cys751 to Serine Change in Accounting for Ligand Selectivity between EGFR and HER-2 at the ATP Site. 287-291 - Milan Pahor:
Implementation of Smooth Continuous Camera Trajectories for Viewing PDB and VRML Objects. 293-299 - Jerome Wielens, Ian T. Crosby, David K. Chalmers:
A Three-dimensional Model of the Human Immunodeficiency Virus Type 1 Integration Complex. 301-317 - Tao Chen, Jie Yang, Yuelang Wang, Chenyang Zhan, Yuhui Zang, Junchuan Qin:
Design of Recombinant Stem Cell Factor-macrophage Colony Stimulating Factor Fusion Proteins and their Biological Activity In Vitro. 319-328 - Danilo Roccatano, Gianluca Sbardella, Massimiliano Aschi, Gianfranco Amicosante, Cecilia Bossa, Alfredo Di Nola, Fernando Mazza:
Dynamical Aspects of TEM-1 β-Lactamase Probed by Molecular Dynamics. 329-340 - Balázs Jójárt, Tamás A. Martinek, Árpád Márki:
The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods. 341-356
Volume 19, Number 6, June 2005
- Gemma K. Kinsella, Isabel Rozas, Graeme Watson:
Modelling the Interaction of Catecholamines with the α1A Adrenoceptor Towards a Ligand-induced Receptor Structure. 357-367 - Yovani Marrero-Ponce, Juan A. Castillo-Garit:
3D-chiral Atom, Atom-type, and Total Non-stochastic and Stochastic Molecular Linear Indices and their Applications to Central Chirality Codification. 369-383 - Nelilma Correia Romeiro, Magaly G. Albuquerque, Ricardo B. de Alencastro, Malini Ravi, Anton J. Hopfinger:
Construction of 4D-QSAR Models for Use in the Design of Novel p38-MAPK Inhibitors. 385-400 - Jordi Muñoz-Muriedas, Samantha Perspicace, Nuria Bech, Salvatore Guccione, Modesto Orozco, F. Javier Luque:
Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient. 401-419 - Claudia Machicado, Jon López-Llano, Santiago Cuesta-López, Marta Bueno, Javier Sancho:
Design of Ligand Binding to an Engineered Protein Cavity Using Virtual Screening and Thermal Up-shift Evaluation. 421-443 - Jeremy R. H. Tame:
Scoring Functions - the First 100 Years. 445-451 - Igor V. Tetko, Johann Gasteiger, Roberto Todeschini, Andrea Mauri, David J. Livingstone, Peter Ertl, Vladimir A. Palyulin, Eugene V. Radchenko, Nikolai S. Zefirov, Alexander S. Makarenko, Vsevolod Yu. Tanchuk, Volodymyr V. Prokopenko:
Virtual Computational Chemistry Laboratory - Design and Description. 453-463
Volume 19, Number 7, July 2005
- Scot Mente, Franco Lombardo:
A recursive-partitioning model for blood-brain barrier permeation. 465-481 - Sukjoon Yoon, Andrew Smellie, David Hartsough, Anton V. Filikov:
Surrogate docking: structure-based virtual screening at high throughput speed. 483-497 - Huanxiang Liu, Xiaojun Yao, Ruisheng Zhang, Mancang Liu, Zhide Hu, Bo Tao Fan:
Prediction of the tissue/blood partition coefficients of organic compounds based on the molecular structure using least-squares support vector machines. 499-508 - Chanin Nantasenamat, Thanakorn Naenna, Chartchalerm Isarankura-Na-Ayudhya, Virapong Prachayasittikul:
Quantitative prediction of imprinting factor of molecularly imprinted polymers by artificial neural network. 509-524 - Laurence Leherte, Nathalie Meurice, Daniel P. Vercauteren:
Influence of conformation on the representation of small flexible molecules at low resolution: alignment of endothiapepsin ligands. 525-549
Volume 19, Number 8, August 2005
- Tran Trung Tran, Jim McKie, Wim Meutermans, Gregory T. Bourne, Peter R. Andrews, Mark L. Smythe:
Topological side-chain classification of β-turns: Ideal motifs for peptidomimetic development. 551-566 - Jianzhong Liu, Liu Yang, Yi Li, Dahua Pan, Anton J. Hopfinger:
Prediction of plasma protein binding of drugs using Kier-Hall valence connectivity indices and 4D-fingerprint molecular similarity analyses. 567-583 - Ignasi Belda, Sergio Madurga, Xavier Llorà, Marc Martinell, Teresa Tarragó, Mireia G. Piqueras, Ernesto Nicolás, Ernest Giralt:
ENPDA: an evolutionary structure-based de novo peptide design algorithm. 585-601 - Dominik Gront, Andrzej Kolinski, Ulrich H. E. Hansmann:
Protein structure prediction by tempering spatial constraints. 603-608 - Daniel J. Kuster, Garland R. Marshall:
Validated ligand mapping of ACE active site. 609-615 - Catherine Koukoulitsa, George D. Geromichalos, Helen Skaltsa:
VolSurf analysis of pharmacokinetic properties for several antifungal sesquiterpene lactones isolated from Greek Centaurea sp. 617-623
Volume 19, Numbers 9-10, September 2005
- Cristian Bologa, Tharun Kumar Allu, Marius Olah, Michael A. Kappler, Tudor I. Oprea:
Descriptor collision and confusion: Toward the design of descriptors to mask chemical structures. 625-635 - Jean-Loup Faulon, W. Michael Brown, Shawn Martin:
Reverse engineering chemical structures from molecular descriptors: how many solutions? 637-650 - Alexandru T. Balaban:
Can topological indices transmit information on properties but not on structures? 651-660 - Anthony Nicholls, J. Andrew Grant:
Molecular shape and electrostatics in the encoding of relevant chemical information. 661-686 - Dominik Kaiser, Barbara Zdrazil, Gerhard F. Ecker:
Similarity-based descriptors (SIBAR) - A tool for safe exchange of chemical information? 687-692 - Alexandre Varnek, Denis Fourches, Frank Hoonakker, Vitaly P. Solov'ev:
Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures. 693-703 - Dmitry Filimonov, Vladimir Poroikov:
Why relevant chemical information cannot be exchanged without disclosing structures. 705-713 - Sergey V. Trepalin, Nikolay Osadchiy:
The centroidal algorithm in molecular similarity and diversity calculations on confidential datasets. 715-729 - Omoshile O. Clement, Osman F. Güner:
Possibilities for transfer of relevant data without revealing structural information. 731-738 - Alan F. Karr, Jun Feng, Xiaodong Lin, Ashish P. Sanil, S. Stanley Young, Jerome P. Reiter:
Secure analysis of distributed chemical databases without data integration. 739-747 - Igor V. Tetko, Ruben Abagyan, Tudor I. Oprea:
Surrogate data - a secure way to share corporate data. 749-764
Volume 19, Number 11, November 2005
- Christophe Chipot, Xavier Rozanska, Surjit B. Dixit:
Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein. 765-770 - Julio Caballero, Miguel Garriga, Michael Fernández:
Genetic neural network modeling of the selective inhibition of the intermediate-conductance Ca2+-activated K+ channel by some triarylmethanes using topological charge indexes descriptors. 771-789 - Andreas Moll, Andreas Hildebrandt, Hans-Peter Lenhof, Oliver Kohlbacher:
BALLView: An object-oriented molecular visualization and modeling framework. 791-800 - Jianguo Wang, Zhengming Li, Ning Ma, Bao-Lei Wang, Lin Jiang, Siew Siew Pang, Yu-Ting Lee, Luke W. Guddat, Ronald G. Duggleby:
Structure-activity relationships for a new family of sulfonylurea herbicides. 801-820 - John Cartmell, Steven J. Enoch, Damjan Krstajic, David E. Leahy:
Automated QSPR through Competitive Workflow. 821-833
Volume 19, Number 12, December 2005
- Zeljko Debeljak, Viktor Marohnic, Goran Srecnik, Marica Medic-Saric:
Novel approach to evolutionary neural network based descriptor selection and QSAR model development. 835-855 - J. Narashima Murthy, M. Nagaraju, G. Madhavi Sastry, A. Raghuram Rao, G. Narahari Sastry:
Active site acidic residues and structural analysis of modelled human aromatase: A potential drug target for breast cancer. 857-870 - Wayne C. Guida, Andrew D. Hamilton, Justin W. Crotty, Saïd M. Sebti:
Protein farnesyltransferase: Flexible docking studies on inhibitors using computational modeling. 871-885 - Vojtech Spiwok, Petra Lipovová, Tereza Skálová, Eva Vondrácková, Jan Dohnálek, Jindrich Hasek, Blanka Králová:
Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance. 887-901
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