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Journal of Computer-Aided Molecular Design, Volume 20
Volume 20, Number 1, January 2006
- Feng Luan, Xiaoyun Zhang, Haixia Zhang, Ruisheng Zhang
, Mancang Liu, Zhide Hu, Bo Tao Fan:
Prediction of standard Gibbs energies of the transfer of peptide anions from aqueous solution to nitrobenzene based on support vector machine and the heuristic method. 1-11 - David Curcó, Francisco Rodríguez-Ropero
Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters. 13-25 - Roman G. Efremov, Yana A. Vereshaga, Pavel E. Volynsky
Association of transmembrane helices: what determines assembling of a dimer? 27-45 - Jan Ziegler, Stephan Schwarzinger
Genetic algorithms as a tool for helix design - computational and experimental studies on prion protein helix 1. 47-54 - Dhilon S. Patel, Prasad V. Bharatam
New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies. 55-66
Volume 20, Number 2, February 2006
- Laurence Miguet, Ziding Zhang
Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors. 67-81 - Antreas Afantitis
Investigation of substituent effect of 1-(3, 3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques. 83-95 - Mihaly Mezei, Marta Filizola
TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations. 97-107 - Ye Che
Development of small molecules designed to modulate protein-protein interactions. 109-130
Volume 20, Number 3, March 2006
- Kristin Tøndel, Endre Anderssen, Finn Drabløs
Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures. 131-144 - Maciej Szaleniec
Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase. 145-157 - Sai Chetan K. Sukuru, Thibaut Crepin
Discovering New Classes of Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change. 159-178 - Giorgio Carta, Valeria Onnis, Andrew J. S. Knox, Darren Fayne
Permuting input for more effective sampling of 3D conformer space. 179-190
Volume 20, Number 4, April 2006
- Roger A. Sayle
Electrostatic evaluation of isosteric analogues. 191-208 - Kathleen M. Gilbert, Carol A. Venanzi:
Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs. 209-225 - Toni Rönkkö, Anu J. Tervo, Jussi Parkkinen, Antti Poso
BRUTUS: Optimization of a grid-based similarity function for rigid-body molecular superposition. II. Description and characterization. 227-236 - Yoshifumi Fukunishi
A Virtual Active Compound Produced from the Negative Image of a Ligand-binding Pocket, and its Application to in-silico Drug Screening. 237-248 - Sung Jin Cho, Yaxiong Sun, William Harte:
ADAAPT: Amgen's data access, analysis, and prediction tools. 249-261
Volume 20, Number 5, May 2006
- Robert A. Beckman, David W. Moreland, Shirley Louise-May, Christine Humblet:
RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case. 263-279 - Zhenshan Zhang, Mingyue Zheng
Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4, 1-benzoxazepinone analogues. 281-293 - Cristina Ferrari, Antonio Macchiarulo
Pharmacophore model for bile acids recognition by the FPR receptor. 295-303 - Marcin Hoffmann
Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors. 305-319 - Masayuki Hata, Garland R. Marshall
Do benzodiazepines mimic reverse-turn structures? 321-331 - Nathan Brown, Ben McKay, Johann Gasteiger:
A novel workflow for the inverse QSPR problem using multiobjective optimization. 333-341
Volume 20, Number 6, June 2006
- Prasanna A. Datar
Comparative residue interaction analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site residues with ligands. 343-360 - Bård Buttingsrud, Einar Ryeng, Ross D. King
Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships. 361-373 - Pavel Banás, Michal Otyepka
Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. 375-383 - Elizabeth A. Kennewell, Peter Willett, Pierre Ducrot, Claude Luttmann:
Identification of target-specific bioisosteric fragments from ligand-protein crystallographic data. 385-394 - Bing Zhang, Vincent B. C. Tan, Kian Meng Lim
Molecular dynamics simulations on the inhibition of Cyclin-Dependent Kinases 2 and 5 in the presence of activators. 395-404
Volume 20, Numbers 7-8, August 2006
- Marta Filizola
Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. 405-416 - Andrei A. Ivanov, Stefano Costanzi
Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling. 417-426 - Sandhya Kortagere, Amitava Roy, Ernest L. Mehler:
Ab initio computational modeling of long loops in G-protein coupled receptors. 427-436 - Masha Y. Niv
Modeling activated states of GPCRs: the rhodopsin template. 437-448 - Francesca Fanelli
Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. 449-461 - Stanley R. Krystek, S. Roy Kimura, Andrew J. Tebben:
Modeling and active site refinement for G protein-coupled receptors: application to the β-2 adrenergic receptor. 463-470 - Nidhi Singh
A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist. 471-493 - Diane L. Lynch, Patricia H. Reggio:
Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer. 495-509 - Marius Wanko, Michael Hoffmann
Computational photochemistry of retinal proteins. 511-518 - Ludovic Renault
Milestones in electron crystallography. 519-527 - Farhad Soltanshahi, Tamsin E. Mansley, Sun Choi
Balancing focused combinatorial libraries based on multiple GPCR ligands. 529-538
Volume 20, Number 9, September 2006
- Ernesto Estrada
Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors. 539-548 - Mingyue Zheng
QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. 549-566 - Nicola J. Richmond, Charlene A. Abrams, Philippa R. N. Wolohan, Edmond J. Abrahamian, Peter Willett, Robert D. Clark
GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D. 567-587 - Tero Huhtiniemi, Carsten Wittekindt, Tuomo Laitinen
Comparative and pharmacophore model for deacetylase SIRT1. 589-599
Volume 20, Numbers 10-11, October 2006
- Demetri Moustakas, P. Therese Lang, Scott C.-H. Pegg, Eric Pettersen, Irwin D. Kuntz, Natasja Brooijmans, Robert C. Rizzo:
Development and validation of a modular, extensible docking program: DOCK 5. 601-619 - Christian D. Klein
Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective. 621-628 - Shayantani Mukherjee, Manju Bansal, Dhananjay Bhattacharyya:
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. 629-645 - Steven L. Dixon, Alexander M. Smondyrev, Eric H. Knoll, Shashidhar N. Rao, David E. Shaw, Richard A. Friesner:
PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. 647-671 - Christian Hallmen, Michael Wiese:
Molecular dynamics simulation of the human adenosine A3 receptor: agonist induced conformational changes of Trp243. 673-684 - Yovani Marrero-Ponce
Bond-based global and local (bond, group and bond-type) quadratic indices and their applications to computer-aided molecular design, 1. QSPR studies of diverse sets of organic chemicals. 685-701
Volume 20, Number 12, December 2006
- Theodora M. Steindl, Daniela Schuster
High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening. 703-715 - Marcus Gastreich
Ultrafast de novo docking combining pharmacophores and combinatorics. 717-734 - Simon J. Cottrell
Incorporating partial matches within multiobjective pharmacophore identification. 735-749 - Gregory A. Landrum
Feature-map vectors: a new class of informative descriptors for computational drug discovery. 751-762 - Jennifer K. Shepphird
A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches. 763-771 - Gerhard Wolber
Efficient overlay of small organic molecules using 3D pharmacophores. 773-788 - Sandhya Kortagere, William J. Welsh:
Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors. 789-802
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