Journal: Journal of Computer-Aided Molecular Design

Volume 20, Issue 9

539 -- 548Ernesto Estrada, Gerardo Díaz, Eduardo J. Delgado. Predicting infinite dilution activity coefficients of organic compounds in water by quantum-connectivity descriptors
549 -- 566Mingyue 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
567 -- 587Nicola J. Richmond, Charlene A. Abrams, Philippa R. N. Wolohan, Edmond J. Abrahamian, Peter Willett 0002, Robert D. Clark. GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D
589 -- 599Tero Huhtiniemi, Carsten Wittekindt, Tuomo Laitinen, Jukka Leppänen, Antero Salminen, Antti Poso, Maija Lahtela-Kakkonen. Comparative and pharmacophore model for deacetylase SIRT1

Volume 20, Issue 7-8

405 -- 416Marta 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
417 -- 426Andrei A. Ivanov, Stefano Costanzi, Kenneth A. Jacobson. Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling
427 -- 436Sandhya Kortagere, Amitava Roy, Ernest L. Mehler. Ab initio computational modeling of long loops in G-protein coupled receptors
437 -- 448Masha Y. Niv, Lucy Skrabanek, Marta Filizola, Harel Weinstein. Modeling activated states of GPCRs: the rhodopsin template
449 -- 461Francesca Fanelli, Pier Giuseppe De Benedetti. Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling
463 -- 470Stanley 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
471 -- 493Nidhi 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
495 -- 509Diane 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
511 -- 518Marius Wanko, Michael Hoffmann, Thomas Frauenheim, Marcus Elstner. Computational photochemistry of retinal proteins
519 -- 527Ludovic 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
529 -- 538Farhad Soltanshahi, Tamsin E. Mansley, Sun Choi, Robert D. Clark. Balancing focused combinatorial libraries based on multiple GPCR ligands

Volume 20, Issue 6

343 -- 360Prasanna 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
361 -- 373Bård Buttingsrud, Einar Ryeng, Ross D. King, Bjørn K. Alsberg. Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships
375 -- 383Pavel 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
385 -- 394Elizabeth A. Kennewell, Peter Willett 0002, Pierre Ducrot, Claude Luttmann. Identification of target-specific bioisosteric fragments from ligand-protein crystallographic data
395 -- 404Bing 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

Volume 20, Issue 5

263 -- 279Robert 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
281 -- 293Zhenshan 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
295 -- 303Cristina Ferrari, Antonio Macchiarulo, Gabriele Costantino, Roberto Pellicciari. Pharmacophore model for bile acids recognition by the FPR receptor
305 -- 319Marcin 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
321 -- 331Masayuki Hata, Garland R. Marshall. Do benzodiazepines mimic reverse-turn structures?
333 -- 341Nathan Brown, Ben McKay, Johann Gasteiger. A novel workflow for the inverse QSPR problem using multiobjective optimization

Volume 20, Issue 4

191 -- 208Roger A. Sayle, Anthony Nicholls. Electrostatic evaluation of isosteric analogues
209 -- 225Kathleen M. Gilbert, Carol A. Venanzi. Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs
227 -- 236Toni 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
237 -- 248Yoshifumi 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
249 -- 261Sung Jin Cho, Yaxiong Sun, William Harte. ADAAPT: Amgen's data access, analysis, and prediction tools

Volume 20, Issue 3

131 -- 144Kristin Tøndel, Endre Anderssen, Finn Drabløs. Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures
145 -- 157Maciej Szaleniec, Malgorzata Witko, Ryszard Tadeusiewicz, Jakub Goclon. Application of artificial neural networks and DFT-based parameters for prediction of reaction kinetics of ethylbenzene dehydrogenase
159 -- 178Sai 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. Brugia malayi Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change
179 -- 190Giorgio Carta, Valeria Onnis, Andrew J. S. Knox, Darren Fayne, David G. Lloyd. Permuting input for more effective sampling of 3D conformer space

Volume 20, Issue 2

67 -- 81Laurence 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
83 -- 95Antreas 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
97 -- 107Mihaly Mezei, Marta Filizola. TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations
109 -- 130Ye Che, Bernard R. Brooks, Garland R. Marshall. Development of small molecules designed to modulate protein-protein interactions

Volume 20, Issue 12

703 -- 715Theodora M. Steindl, Daniela Schuster, Gerhard Wolber, Christian Laggner, Thierry Langer. High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening
717 -- 734Marcus Gastreich, Markus Lilienthal, Hans Briem, Holger Claussen. Ultrafast de novo docking combining pharmacophores and combinatorics
735 -- 749Simon J. Cottrell, Valerie J. Gillet, Robin Taylor. Incorporating partial matches within multiobjective pharmacophore identification
751 -- 762Gregory A. Landrum, Julie Penzotti, Santosh Putta. Feature-map vectors: a new class of informative descriptors for computational drug discovery
763 -- 771Jennifer K. Shepphird, Robert D. Clark. A marriage made in torsional space: using GALAHAD models to drive pharmacophore multiplet searches
773 -- 788Gerhard Wolber, Alois A. Dornhofer, Thierry Langer. Efficient overlay of small organic molecules using 3D pharmacophores
789 -- 802Sandhya Kortagere, William J. Welsh. Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors

Volume 20, Issue 10-11

601 -- 619Demetri 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
621 -- 628Christian D. Klein, Anke Bachelier. Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective
629 -- 645Shayantani Mukherjee, Manju Bansal, Dhananjay Bhattacharyya. Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis
647 -- 671Steven 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
673 -- 684Christian Hallmen, Michael Wiese. 3 receptor: agonist induced conformational changes of Trp243
685 -- 701Yovani Marrero-Ponce, Francisco Torrens, Ysaias J. 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

Volume 20, Issue 1

1 -- 11Feng 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
13 -- 25David Curcó, Francisco Rodríguez-Ropero, Carlos Alemán. Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters
27 -- 45Roman G. Efremov, Yana A. Vereshaga, Pavel E. Volynsky, Dmitry E. Nolde, Alexander S. Arseniev. Association of transmembrane helices: what determines assembling of a dimer?
47 -- 54Jan Ziegler, Stephan Schwarzinger. Genetic algorithms as a tool for helix design - computational and experimental studies on prion protein helix 1
55 -- 66Dhilon S. Patel, Prasad V. Bharatam. New leads for selective GSK-3 inhibition: pharmacophore mapping and virtual screening studies