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ORCIDJournal of Computer-Aided Molecular Design, Volume 15
Volume 15, Number 1, January 2001
- Osvaldo Andrade Santos-Filho
, Anton J. Hopfinger:
A search for sources of drug resistance by the 4D-QSAR analysis of a set of antimalarial dihydrofolate reductase inhibitors. 1-12 - Bruno O. Villoutreix, David G. Covell, Anna M. Blom, Anders Wallqvist, Ute Friedrich, Björn Dahlbäck:
Screening the molecular surface of human anticoagulant protein C: A search for interaction sites. 13-27 - Irini A. Doytchinova:
CoMFA-based comparison of two models of binding site on adenosine A1 receptor. 29-39 - Keun Woo Lee, James M. Briggs:
Comparative molecular field analysis (CoMFA) study of epothilones - tubulin depolymerization inhibitors: Pharmacophore development using 3D QSAR methods. 41-55 - Fabrizio Melani, Paola Gratteri, Michele Adamo, Claudia Bonaccini:
FILO (Field Interaction Ligand Optimization): A simplex strategy for searching the optimal ligand interaction field in drug design. 57-66 - Ana Gallegos Saliner, David Robert, Xavier Gironés, Ramon Carbó-Dorca:
Structure-toxicity relationships of polycyclic aromatic hydrocarbons using molecular quantum similarity. 67-80 - J. E. J. Mills, Iwan J. P. de Esch, Tim D. J. Perkins, Philip M. Dean:
Slate: A method for the superposition of flexible ligands. 81-96
Volume 15, Number 2, February 2001
- Didier Rognan, Seema Mukhija, Gerd Folkers, Oliver Zerbe:
NMR-restrained docking of a peptidic inhibitor to the N-terminal domain of the phosphoenolpyruvate: sugar phosphotransferase enzyme I. 103-115 - Anna Bernardi, Marta Galgano, Laura Belvisi, Giorgio Colombo:
Simulation of carbohydrate-protein interactions: Computer-aided design of a second generation GM1 mimic. 117-128 - Christopher J. Woods, Michael A. King, Jonathan W. Essex:
The configurational dependence of binding free energies: A Poisson-Boltzmann study of Neuraminidase inhibitors. 129-144 - Lu Wang, Yong Duan, Pieter F. W. Stouten, George V. De Lucca, Ronald M. Klabe, Peter A. Kollman:
Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations. 145-156 - Laurent David, Ray Luo, Michael K. Gilson:
Ligand-receptor docking with the Mining Minima optimizer. 157-171 - Ross D. King, Ashwin Srinivasan, Luc Dehaspe:
Warmr: a data mining tool for chemical data. 173-181 - L. A. Poveda, V. R. Ferro, José Manuel García de la Vega, Raúl H. González-Jonte:
A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins. 183-193
Volume 15, Number 3, March 2001
- Antti Poso, Jukka Gynther, Risto Juvonen:
A comparative molecular field analysis of cytochrome P450 2A5 and 2A6 inhibitors. 195-202 - Enrica Filipponi, Gabriele Cruciani, Oriana Tabarrini, Violetta Cecchetti, Arnaldo Fravolini:
QSAR study and VolSurf characterization of anti-HIV quinolone library. 203-217 - Giuseppe Musumarra, Daniele F. Condorelli, Alessandro S. Costa, Maria Fichera:
A multivariate insight into the in vitro antitumour screen database of the National Cancer Institute: classification of compounds, similarities among cell lines and the influence of molecular targets. 219-234 - Adriana M. Namba, Salvador León, Gil Valdo José da Silva, Carlos Alemán:
Force-field parametrization and molecular dynamics simulations of p-menthan-3, 9-diols: a family of amphiphilic compounds derived from terpenoids. 235-245 - Janne E. Tønder, Preben H. Olesen, John Bondo Hansen, Mikael Begtrup, Ingrid Pettersson:
An improved nicotinic pharmacophore and a stereoselective CoMFA-model for nicotinic agonists acting at the central nicotinic acetylcholine receptors labelled by [3H]-N-methylcarbamylcholine. 247-258 - Margie M. Nair, Graham E. Jackson, Gerd Gäde:
Conformational study of insect adipokinetic hormones using NMR constrained molecular dynamics. 259-270 - Han van de Waterbeemd, Dennis A. Smith, Barry C. Jones:
Lipophilicity in PK design: methyl, ethyl, futile. 273-286
Volume 15, Number 4, April 2001
- Hülya Yekeler:
Solvent effects on dimeric self-association of 2-pyrrolidinone: An ab initio study. 287-295 - Marta Filizola, Hugo O. Villar, Gilda H. Loew:
Differentiation of delta, µ, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties. 297-307 - Elsa S. Henriques, Wely B. Floriano, Nathalie Reuter, André Melo, David Brown, José A. N. F. Gomes, Bernard Maigret, Marco A. C. Nascimento, Maria João Ramos:
The search for a new model structure of beta-Factor XIIa. 309-322 - Ming-Ju Huang, Jerzy Leszczynski:
An ab initio theoretical study of the stereoisomers of tetrahydrocannabinols. 323-333 - Raimund Mannhold, Han van de Waterbeemd:
Substructure and whole molecule approaches for calculating log P. 337-354 - Andreas Klamt, Frank Eckert, Martin Hornig:
COSMO-RS: A novel view to physiological solvation and partition questions. 355-365 - Ki H. Kim:
Thermodynamic aspects of hydrophobicity and biological QSAR. 367-380 - Glen Eugene Kellogg, James C. Burnett, Donald J. Abraham:
Very empirical treatment of solvation and entropy: a force field derived from Log Po/w. 381-393
Volume 15, Number 5, May 2001
- Wolfgang Sippl, Jean-Marie Contreras, Isabelle Parrot, Yveline M. Rival, Camille G. Wermuth:
Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors. 395-410 - Todd J. A. Ewing, Shingo Makino, A. Geoffrey Skillman, Irwin D. Kuntz:
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. 411-428 - Peng Tao, Luhua Lai:
Protein ligand docking based on empirical method for binding affinity estimation. 429-446 - Jiang Zhu, Haibo Yu, Hao Fan, Haiyan Liu, Yunyu Shi:
Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks. 447-463 - Massimo Bertelli, Eman El-Bastawissy, Michael H. Knaggs, Michael P. Barrett, Stefania Hanau, Ian H. Gilbert:
Selective inhibition of 6-phosphogluconate dehydrogenase from Trypanosoma brucei. 465-475 - José M. Mas, Patrick Aloy, Marc A. Martí-Renom, Baldomero Oliva, R. de Llorens, Francesc X. Avilés, Enrique Querol:
Classification of protein disulphide-bridge topologies. 477-487 - Pascal Furet, Thomas Meyer, Peer R. E. Mittl, Heinz Fretz:
Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching. 489-495
Volume 15, Number 6, June 2001
- Matthias Rarey, Martin Stahl:
Similarity searching in large combinatorial chemistry spaces. 497-520 - Xavier de la Cruz, Miquel Calvo:
Use of surface area computations to describe atom-atom interactions. 521-532 - Robert P. Bywater, David Thomas, Gert Vriend:
A sequence and structural study of transmembrane helices. 533-552 - Shingo Makino, Takashi Kayahara, Kazumi Tashiro, Mitsuo Takahashi, Takashi Tsuji, Masataka Shoji:
Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique. 553-559 - M. J. Duart, Ramón García-Domenech, G. M. Antón-Fos, Jorge Gálvez:
Optimization of a mathematical topological pattern for the prediction of antihistaminic activity. 561-572 - Jun Zeng, Herbert R. Treutlein, George B. Rudy:
Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach. 573-586
Volume 15, Number 7, July 2001
- Michael Pitman, Wolfgang Huber, Hans W. Horn, Andreas Krämer, Julia E. Rice, William C. Swope:
FLASHFLOOD: A 3D Field-based similarity search and alignment method for flexible molecules. 587-612 - Sung-Sau So, Martin Karplus:
Evaluation of designed ligands by a multiple screening method: Application to glycogen phosphorylase inhibitors constructed with a variety of approaches. 613-647 - György M. Keserü:
A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. 649-657 - Richard D. Beger, Jon G. Wilkes:
Developing 13C NMR quantitative spectrometric data-activity relationship (QSDAR) models of steroid binding to the corticosteroid binding globulin. 659-669 - Sunil Gupta, Manjit Singh, A. K. Madan:
Predicting anti-HIV activity: computational approach using a novel topological descriptor. 671-678
Volume 15, Number 8, August 2001
- Daniel J. Price, William L. Jorgensen:
Improved convergence of binding affinities with free energy perturbation: Application to nonpeptide ligands with pp60src SH2 domain. 681-695 - Yiannis N. Kaznessis, Mark E. Snow, C. John Blankley:
Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water. 697-708 - Francisco Torrens:
A new topological index to elucidate apolar hydrocarbons. 709-719 - Joaquim Mendes, António M. Baptista, Maria Arménia Carrondo, Cláudio M. Soares:
Implicit solvation in the self-consistent mean field theory method: sidechain modelling and prediction of folding free energies of protein mutants. 721-740 - David J. Livingstone, Martyn G. Ford, Jarmo J. Huuskonen, David W. Salt:
Simultaneous prediction of aqueous solubility and octanol/water partition coefficient based on descriptors derived from molecular structure. 741-752 - Peter Aadal Nielsen, Tommy Liljefors:
Conformational analysis of kainate in aqueous solution in relation to its binding to AMPA and kainic acid receptors. 753-763
Volume 15, Number 9, September 2001
- Pierre Ducrot, Charles R. Andrianjara, Roger Wrigglesworth:
CoMFA and CoMSIA 3D-quantitative structure-activity relationship model on benzodiazepine derivatives, inhibitors of phosphodiesterase IV. 767-785 - Osvaldo Andrade Santos-Filho, Rama K. Mishra, Anton J. Hopfinger:
Free energy force field (FEFF) 3D-QSAR analysis of a set of Plasmodium falciparum dihydrofolate reductase inhibitors. 787-810 - Robert Preissner, Andrean Goede, Kristian Rother, F. Osterkamp, U. Koert, Cornelius Frömmel:
Matching organic libraries with protein-substructures. 811-817 - Miguel Coll, Juan Frau, Bartolomé Vilanova, Josefa Donoso, Francisco Muñoz:
Electrostatic and structural similarity of classical and non-classical lactam compounds. 819-833 - Paul Watson, Peter Willett, Valerie J. Gillet, Marcel L. Verdonk:
Calculating the knowledge-based similarity of functional groups using crystallographic data. 835-857 - Orazio Nicolotti, Marialuisa Pellegrini-Calace, Antonio Carrieri, Cosimo Damiano Altomare, Nuria B. Centeno, Ferran Sanz, Andrea Carotti:
Neuronal nicotinic receptor agonists: a multi-approach development of the pharmacophore. 859-872
Volume 15, Number 10, October 2001
- Stephen Hanessian, Nicolas Moitessier, Eric Therrien:
A comparative docking study and the design of potentially selective MMP inhibitors. 873-881 - Richard E. Wilcox, J. Eric Ragan, Robert S. Pearlman, Mi Youn Kim Brusniak, R. M. Eglen, D. W. Bonhaus, Thomas E. Tenner Jr., J. D. Miller:
High-affinity interactions of ligands at recombinant Guinea pig 5HT7 receptors. 883-909 - Scott C.-H. Pegg, Jose J. Haresco, Irwin D. Kuntz:
A genetic algorithm for structure-based de novo design. 911-933 - Ryan Bitetti-Putzer, Diane Joseph-McCarthy, James M. Hogle, Martin Karplus:
Functional group placement in protein binding sites: a comparison of GRID and MCSS. 935-960
Volume 15, Number 11, November 2001
- Mahindra T. Makhija, Vithal M. Kulkarni:
Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR. 961-978 - Jiang Zhu, Hao Fan, Haiyan Liu, Yunyu Shi:
Structure-based ligand design for flexible proteins: Application of new F-DycoBlock. 979-996 - Supa Hannongbua, Sirikanok Prasithichokekul, Pornpan Pungpo:
Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations. 997-1004 - Agnieszka Bronowska, Zdzislaw Chilmonczyk, Andrzej Les, Øyvind Edvardsen, Roy Østensen, Ingebrigt Sylte:
Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues. 1005-1023 - María L. López-Rodríguez, Marta Murcia, Bellinda Benhamú, Mireia Olivella, Mercedes Campillo, Leonardo Pardo:
Computational Model of the Complex between GR113808 and the 5-HT4 Receptor Guided by Site-Directed Mutagenesis and the Crystal Structure of Rhodopsin. 1025-1033 - Elizabeth E. Howell, Ushma Shukla, Stephanie N. Hicks, R. Derike Smiley, Leslie A. Kuhn, Maria I. Zavodszky:
One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme. 1035-1052
Volume 15, Number 12, December 2001
- Xavier Gironés, Ana Gallegos Saliner, Ramon Carbó-Dorca:
Antimalarial activity of synthetic 1, 2, 4-trioxanes and cyclic peroxy ketals, a quantum similarity study. 1053-1063 - Miklos Feher, Jonathan M. Schmidt:
Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling. 1065-1083 - Artur Gieldon, Rajmund Kazmierkiewicz, Rafal Slusarz, Jerzy Ciarkowski:
Molecular modeling of interactions of the non-peptide antagonist YM087 with the human vasopressin V1a, V2 receptors and with oxytocin receptors. 1085-1104 - Martha S. Head, M. Dominic Ryan, Dennis Lee, Yanhong Feng, Cheryl A. Janson, Nestor O. Concha, Paul M. Keller, Walter E. deWolf Jr.:
Structure-based combinatorial library design: Discovery of non-peptidic inhibitors of caspases 3 and 8. 1105-1117 - Jonathan B. Baell, Stewart A. Forsyth, Robert W. Gable, Raymond S. Norton, Roger J. Mulder:
Design and synthesis of type-III mimetics of omega-conotoxin GVIA. 1119-1136 - Jonas Boström:
Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools. 1137-1152 - Orazio Nicolotti, Marialuisa Pellegrini-Calace, Antonio Carrieri, Cosimo Damiano Altomare, Nuria B. Centeno, Ferran Sanz, Andrea Carotti:
Erratum to 'Neuronal nicotinic receptor agonists: a multi-approach development of the pharmacophore' [J. Comput. Aid. Mol. Des., Vol. 15 (2001) 859]. 1153
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