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daevans docking [37 articles]

Recent papers added to daevans library classified by the tag docking. You can also see everyone's docking.
  • Ligand-Protein Docking with Water Molecules
    J. Chem. Inf. Model. (23 January 2008)
    by BC Roberts, RL Mancera
    posted to docking water by daevans on 2008-02-14 20:34:04 as ** along with 2 people BragilMassoud middledomain
  • Similarity Based Docking.
    J Chem Inf Model (29 November 2007)
    by J Marialke, S Tietze, Joannis Apostolakis
    posted to docking overlay by daevans on 2007-12-05 08:54:00 as ** along with 2 people sim82 apostola
  • Tagged Fragment Method for Evolutionary Structure-Based De Novo Lead Generation and Optimization
    J. Med. Chem., Vol. 50, No. 22. (1 November 2007), pp. 5392-5402.
    by Q Liu, B Masek, K Smith, J Smith
    posted to denovo docking by daevans on 2007-12-04 08:53:27 as **
  • Target Specific Virtual Screening: Optimization of an Estrogen Receptor Screening Platform
    J. Med. Chem., Vol. 50, No. 22. (1 November 2007), pp. 5301-5310.
    by AJS Knox, MJ Meegan, V Sobolev, D Frost, DM Zisterer, DC Williams, DG Lloyd
    posted to docking virtual_screening by daevans on 2007-12-04 08:52:12 as **
  • Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects.
    J Med Chem, Vol. 49, No. 2. (26 January 2006), pp. 534-553.
    by Woody Sherman, Tyler Day, Matthew P Jacobson, Richard A Friesner, Ramy Farid
    posted to docking induced_fit by daevans on 2007-11-29 13:16:33 as ** along with 3 people and 1 group BragilMassoud yongzhao kazemi TSRI_MGL
  • A Flexible Approach to Induced Fit Docking
    J. Med. Chem. (22 November 2007)
    by Sander B Nabuurs, Markus Wagener, Jacob de Vlieg
    posted to docking induced_fit by daevans on 2007-11-29 13:14:00 as **
  • Grand canonical monte carlo simulation of ligand-protein binding.
    J Chem Inf Model, Vol. 46, No. 1. (b 2006), pp. 231-242.
    by M Clark, F Guarnieri, I Shkurko, J Wiseman
    posted to docking scoring simulation by daevans on 2007-11-03 17:47:25 as ** along with 1 person ttjoseph
  • Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy
    J. Chem. Inf. Model. (23 October 2007)
    by JJ Sutherland, RK Nandigam, JA Erickson, M Vieth
    posted to docking flexible rocs by daevans on 2007-10-25 22:51:13 as ** along with 1 person schlauchi
  • Consensus Adaptation of Fields for Molecular Comparison (AFMoC) Models Incorporate Ligand and Receptor Conformational Variability into Tailor-made Scoring Functions
    J. Chem. Inf. Model. (25 October 2007)
    by B Breu, K Silber, H Gohlke
    posted to 3dqsar afmoc docking homology by daevans on 2007-10-25 22:50:15 as ** along with 1 person middledomain
  • Prediction of protein-ligand complex structure by docking software guided by other complex structures
    Journal of Molecular Graphics and Modelling, Vol. In Press, Corrected Proof
    by Yoshifumi Fukunishi, Haruki Nakamura
    posted to docking knowledge-based by daevans on 2007-10-23 10:05:11 as **
  • Prediction of the 3D Structure and Dynamics of Human DP G-Protein Coupled Receptor Bound to an Agonist and an Antagonist
    J. Am. Chem. Soc., Vol. 129, No. 35. (5 September 2007), pp. 10720-10731.
    by Y Li, F Zhu, N Vaidehi, WA Goddard, F Sheinerman, S Reiling, I Morize, L Mu, K Harris, A Ardati, A Laoui
    posted to docking gpcr homology sbdd by daevans on 2007-10-05 14:34:41 as ** along with 1 person superpyrin
  • Mechanism-Based Thrombin Inhibitors: Design, Synthesis, and Molecular Docking of a New Selective 2-Oxo-2H-1-benzopyran Derivative
    J. Med. Chem., Vol. 50, No. 15. (26 July 2007), pp. 3645-3650.
    by R Frederick, S Robert, C Charlier, J Wouters, B Masereel, L Pochet
    posted to docking sbdd by daevans on 2007-08-23 10:30:10 as **
  • Structure-based activity prediction for an enzyme of unknown function
    Nature (01 July 2007)
    by Johannes C Hermann, Ricardo Marti-Arbona, Alexander A Fedorov, Elena Fedorov, Steven C Almo, Brian K Shoichet, Frank M Raushel
    posted to docking by daevans on 2007-08-21 13:38:27 as ** along with 6 people aheilbut tjimenez zwang pkolb kimicc ivke
  • Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
    Journal of Molecular Biology, Vol. 371, No. 4. (24 August 2007), pp. 1118-1134.
    by David L Mobley, Alan P Graves, John D Chodera, Andrea C Mcreynolds, Brian K Shoichet, Ken A Dill
    posted to docking scoring simulation by daevans on 2007-08-15 22:10:16 as ** along with 4 people and 3 groups barry insilico superpyrin dmobley structural_bioinformatics Bioinformatics Computer Aided Drug Design
  • Classification of Water Molecules in Protein Binding Sites
    J. Am. Chem. Soc., Vol. 129, No. 9. (7 March 2007), pp. 2577-2587.
    by C Barillari, J Taylor, R Viner, JW Essex
    posted to docking simulation water by daevans on 2007-08-14 17:11:18 as ** along with 3 people LamBras jteyra dmobley
  • Supervised Scoring Models with Docked Ligand Conformations for Structure-Based Virtual Screening
    J. Chem. Inf. Model. (9 August 2007)
    by R Teramoto, H Fukunishi
    posted to docking machine_learning scoring by daevans on 2007-08-10 16:16:04 as **
  • Multistructure 3D-QSAR Studies on a Series of Conformationally Constrained Butyrophenones Docked into a New Homology Model of the 5-HT2A Receptor
    J. Med. Chem., Vol. 50, No. 14. (12 July 2007), pp. 3242-3255.
    by C Dezi, J Brea, M Alvarado, E Ravina, CF Masaguer, MI Loza, F Sanz, M Pastor
    posted to 3dqsar docking homology by daevans on 2007-07-08 18:47:42 as **
  • P2Y1 Antagonists: Combining Receptor-Based Modeling and QSAR for a Quantitative Prediction of the Biological Activity Based on Consensus Scoring
    J. Med. Chem., Vol. 50, No. 14. (12 July 2007), pp. 3229-3241.
    by S Costanzi, IG Tikhonova, M Ohno, EJ Roh, BV Joshi, AO Colson, D Houston, S Maddileti, TK Harden, KA Jacobson
    posted to 3dqsar docking gpcr homology by daevans on 2007-07-08 18:44:19 as **
  • Design, synthesis, binding, and molecular modeling studies of new potent ligands of cannabinoid receptors
    Bioorganic & Medicinal Chemistry, Vol. 15, No. 16. (15 August 2007), pp. 5406-5416.
    by Antonella Brizzi, Maria G Cascio, Vittorio Brizzi, Tiziana Bisogno, Maria T Dinatolo, Adriano Martinelli, Tiziano Tuccinardi, Vincenzo Di Marzo
    posted to docking homology by daevans on 2007-07-08 12:23:20 as **
  • Comparison of Topological, Shape, and Docking Methods in Virtual Screening.
    J Chem Inf Model (26 June 2007)
    by Georgia B McGaughey, Robert P Sheridan, Christopher I Bayly, J C Culberson, Constantine Kreatsoulas, Stacey Lindsley, Vladimir Maiorov, Jean-Francois F Truchon, Wendy D Cornell
    posted to docking rocs virtual_screening by daevans on 2007-06-29 13:37:56 as ** along with 5 people and 1 group ucbcjbm thanatos BragilMassoud steff83 middledomain Computer Aided Drug Design
  • Synthesis, docking studies and anti-inflammatory activity of 4,5,6,7-tetrahydro-2H-indazole derivatives
    Bioorganic & Medicinal Chemistry, Vol. 15, No. 10. (15 May 2007), pp. 3463-3473.
    by Ornelio Rosati, Massimo Curini, Maria C Marcotullio, Antonio Macchiarulo, Marina Perfumi, Laura Mattioli, Francesco Rismondo, Giancarlo Cravotto
    posted to cox2 docking by daevans on 2007-04-12 15:06:07 as **
  • Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm.
    J Am Chem Soc, Vol. 126, No. 40. (13 October 2004), pp. 13156-13164.
    by CE Chang, MK Gilson
    posted to docking by daevans on 2007-03-08 22:58:46 as ** along with 2 people kentsis dmobley
  • Diverse, high-quality test set for the validation of protein-ligand docking performance.
    J Med Chem, Vol. 50, No. 4. (22 February 2007), pp. 726-741.
    by MJ Hartshorn, ML Verdonk, G Chessari, SC Brewerton, WT Mooij, PN Mortenson, CW Murray
    posted to docking test_set by daevans on 2007-02-18 20:38:30 as ** along with 5 people thanatos BragilMassoud ramensky hmk superpyrin
  • Comparison of Shape-Matching and Docking as Virtual Screening Tools
    J. Med. Chem., Vol. 50, No. 1. (11 January 2007), pp. 74-82.
    by PCD Hawkins, AG Skillman, A Nicholls
    posted to docking rocs virtual_screening by daevans on 2007-01-05 07:06:00 as *** along with 5 people thanatos BragilMassoud nachtalp apostola schlauchi
  • 3D QSAR Selectivity Analyses of Carbonic Anhydrase Inhibitors: Insights for the Design of Isozyme Selective Inhibitors
    J. Chem. Inf. Model., Vol. 46, No. 6. (27 November 2006), pp. 2737-2760.
    by A Weber, M Bohm, CT Supuran, A Scozzafava, CA Sotriffer, G Klebe
    posted to 3dqsar docking by daevans on 2006-12-17 14:31:28 as ** along with 1 person schuwi
  • Benchmarking Sets for Molecular Docking
    J. Med. Chem. (26 October 2006)
    by N Huang, BK Shoichet, JJ Irwin
    posted to docking dud test_set by daevans on 2006-11-21 22:10:38 as ** along with 2 people and 1 group BragilMassoud yongzhao TSRI_MGL
  • Do Structurally Similar Ligands Bind in a Similar Fashion?
    J. Med. Chem., Vol. 49, No. 23. (16 November 2006), pp. 6716-6725.
    by J Bostrom, A Hogner, S Schmitt
    posted to binding_modes docking by daevans on 2006-11-21 22:09:48 as ** along with 3 people nickolay schlauchi superpyrin
  • Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
    J. Med. Chem. (23 September 2006)
    by RA Friesner, RB Murphy, MP Repasky, LL Frye, JR Greenwood, TA Halgren, PC Sanschagrin, DT Mainz
    posted to docking glide_xp scoring by daevans on 2006-11-06 16:33:08 as *** along with 4 people BragilMassoud dgruiz LamBras middledomain
  • Homology model directed alignment selection for comparative molecular field analysis: Application to photosystem II inhibitors
    Journal of Computer-Aided Molecular Design, Vol. V14, No. 2. (1 February 2000), pp. 181-197.
    by Mehran Jalaie, Jon A Erickson
    posted to 3dqsar comfa docking by daevans on 2006-10-27 17:14:56 as **
  • Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.
    J Med Chem, Vol. 47, No. 1. (1 January 2004), pp. 45-55.
    by JA Erickson, M Jalaie, DH Robertson, RA Lewis, M Vieth
    posted to docking flexible by daevans on 2006-10-27 17:00:15 as ** along with 5 people and 3 groups BragilMassoud apaydin yongzhao sangeetha kazemi Bioinformatics TSRI_MGL insilicodrug
  • On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
    Journal of Chemical Information and Modelling, Vol. 46 (2006), pp. 401-415.
    by H Chen, PD Lyne, F Giordametto, T Lovell, J Li
    posted to docking icm scoring by daevans on 2006-10-07 15:39:14 as **
  • Parameter Estimation for Scoring Protein-Ligand Interactions Using Negative Training Data
    J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5856-5868.
    by TA Pham, AN Jain
    posted to docking scoring surflex-dock by daevans on 2006-09-29 13:50:46 as *** along with 1 person schlauchi
  • A Critical Assessment of Docking Programs and Scoring Functions
    J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5912-5931.
    by GL Warren, CW Andrews, AM Capelli, B Clarke, J Lalonde, MH Lambert, M Lindvall, N Nevins, SF Semus, S Senger, G Tedesco, ID Wall, JM Woolven, CE Peishoff, MS Head
    posted to docking scoring by daevans on 2006-09-29 13:48:46 as ** along with 5 people BragilMassoud aalibes chad_davis schlauchi superpyrin
  • A Novel Computational Analysis of Ligand-Induced Conformational Changes in the ATP Binding Sites of Cyclin Dependent Kinases
    J. Med. Chem., Vol. 49, No. 18. (7 September 2006), pp. 5434-5441.
    by J Subramanian, S Sharma, C B-Rao
    posted to docking flexible knowledge-based by daevans on 2006-08-31 15:40:46 as read
  • Virtual Screening of DNA Minor Groove Binders
    J. Med. Chem., Vol. 49, No. 14. (13 July 2006), pp. 4232-4238.
    by DA Evans, S Neidle
    posted to docking scoring by daevans on 2006-08-31 09:56:52 as read
  • An Integrated in Silico 3D Model-Driven Discovery of a Novel, Potent, and Selective Amidosulfonamide 5-HT<sub>1A</sub> Agonist (PRX-00023) for the Treatment of Anxiety and Depression
    J. Med. Chem., Vol. 49, No. 11. (1 June 2006), pp. 3116-3135.
    by OM Becker, DS Dhanoa, Y Marantz, D Chen, S Shacham, S Cheruku, A Heifetz, P Mohanty, M Fichman, A Sharadendu, R Nudelman, M Kauffman, S Noiman
    posted to docking gpcr homology modelling by daevans on 2006-08-30 16:04:39 as read
  • Novel Structural Features of CDK Inhibition Revealed by an ab Initio Computational Method Combined with Dynamic Simulations.
    J Med Chem, Vol. 49, No. 17. (24 August 2006), pp. 5141-5153.
    by Lucy Heady, Marivi Fernandez-Serra, Ricardo L Mancera, Sian Joyce, Ashok R Venkitaraman, Emilio Artacho, Chris-Kriton K Skylaris, Lucio C Ciacchi, Mike C Payne
    posted to castep docking function scoring by daevans on 2006-08-30 16:03:09 as *** along with 1 person BragilMassoud
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