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ORCIDJournal 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, Carlos Alemán:
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, Dmitry E. Nolde, Alexander S. Arseniev:
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, Maryse Barbier, Martin G. Grigorov:
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, Georgia Melagraki, Haralambos Sarimveis, Panayiotis A. Koutentis, John Markopoulos, Olga Igglessi-Markopoulou:
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, Bernard R. Brooks, Garland R. Marshall:
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, Malgorzata Witko, Ryszard Tadeusiewicz, Jakub Goclon:
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, Youli Milev, Liesl C. Marsh, Jonathan B. Hill, Regan J. Anderson, Jonathan C. Morris, Anjali Rohatgi, Gavin O'Mahony, Morten Grøtli, Franck Danel, Malcolm G. P. Page, Michael Härtlein, Stephen Cusack, Michael A. Kron, Leslie A. Kuhn:
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, David G. Lloyd:
Permuting input for more effective sampling of 3D conformer space. 179-190
Volume 20, Number 4, April 2006
- Roger A. Sayle, Anthony Nicholls:
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, Satoru Kubota, Chisato Kanai, Haruki Nakamura:
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, Li Du, Jianhua Shen, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang:
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, Gabriele Costantino, Roberto Pellicciari:
Pharmacophore model for bile acids recognition by the FPR receptor. 295-303 - Marcin Hoffmann, Krystian Eitner, Marcin von Grotthuss, Leszek Rychlewski, Ewa Banachowicz, Tomasz Grabarkiewicz, Tomasz Szkoda, Andrzej Kolinski:
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, Santosh A. Khedkar, Alpeshkumar K. Malde, Evans C. Coutinho:
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, Bjørn K. Alsberg:
Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships. 361-373 - Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský:
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, Tong Earn Tay:
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, Simon X. Wang, Harel Weinstein:
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, Kenneth A. Jacobson:
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, Lucy Skrabanek, Marta Filizola, Harel Weinstein:
Modeling activated states of GPCRs: the rhodopsin template. 437-448 - Francesca Fanelli, Pier Giuseppe De Benedetti:
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, Gwénaël Chevé, David M. Ferguson, Christopher R. McCurdy:
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, Thomas Frauenheim, Marcus Elstner:
Computational photochemistry of retinal proteins. 511-518 - Ludovic Renault, Hui-Ting Chou, Po-Lin Chiu, Rena M. Hill, Xiangyan Zeng, Bryant Gipson, Zi Yan Zhang, An-Chi Chen, Vinzenz Unger, Henning Stahlberg:
Milestones in electron crystallography. 519-527 - Farhad Soltanshahi, Tamsin E. Mansley, Sun Choi, Robert D. Clark:
Balancing focused combinatorial libraries based on multiple GPCR ligands. 529-538
Volume 20, Number 9, September 2006
- Ernesto Estrada, Gerardo Díaz, Eduardo J. Delgado:
Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors. 539-548 - Mingyue Zheng, Kunqian Yu, Hong Liu, Xiaomin Luo, Kaixian Chen, Weiliang Zhu, Hualiang Jiang:
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, Jukka Leppänen, Antero Salminen, Antti Poso, Maija Lahtela-Kakkonen:
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, Anke Bachelier:
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, Francisco Torrens, Ysaias José Alvarado, Richard Rotondo:
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, Gerhard Wolber, Christian Laggner, Thierry Langer:
High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening. 703-715 - Marcus Gastreich, Markus Lilienthal, Hans Briem, Holger Claussen:
Ultrafast de novo docking combining pharmacophores and combinatorics. 717-734 - Simon J. Cottrell, Valerie J. Gillet, Robin Taylor:
Incorporating partial matches within multiobjective pharmacophore identification. 735-749 - Gregory A. Landrum, Julie Penzotti, Santosh Putta:
Feature-map vectors: a new class of informative descriptors for computational drug discovery. 751-762 - Jennifer K. Shepphird, Robert D. Clark:
A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches. 763-771 - Gerhard Wolber, Alois A. Dornhofer, Thierry Langer:
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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