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dmobley library [162 articles]

最近 dmobley さんのライブラリ .
  • Entropy and Free Energy of a Mobile Protein Loop in Explicit Water
    J. Phys. Chem. B (10 July 2008)
    by Srinath Cheluvaraja, Mihail Mihailescu, Hagai Meirovitch
    posted to methodology entropy by dmobley on 2008-07-11 21:15:02 as **
  • Optimization of Azoles as Anti-Human Immunodeficiency Virus Agents Guided by Free-Energy Calculations
    J. Am. Chem. Soc. (28 June 2008)
    by Jacob G Zeevaart, Ligong Wang, Vinay V Thakur, Cheryl S Leung, Julian Tirado-Rives, Christopher M Bailey, Robert A Domaoal, Karen S Anderson, William L Jorgensen
    posted to relative free_energy application by dmobley on 2008-07-08 17:07:03 as **
  • Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides
    The Journal of Chemical Physics, Vol. 129, No. 1. (2008)
    by Zanxia Cao, Haiyan Liu
    posted to methodology free_energy conformation by dmobley on 2008-07-08 16:53:14 as **
  • Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy
    The Journal of Chemical Physics, Vol. 129, No. 1. (2008)
    by Lianqing Zheng, Wei Yang
    posted to methods free_energy by dmobley on 2008-07-08 16:50:25 as **
  • The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Paul Labute
    posted to hydration gb free_energy by dmobley on 2008-07-03 01:23:30 as ** along with 4 people and 1 group sobolevnrm RamuAnandakrishnan middledomain sunhwan baker-group
  • Variance Minimization of Free Energy Estimates from Optimized Expanded Ensembles
    J. Phys. Chem. B (14 June 2008)
    by Francisco J Martínez-Veracoechea, Fernando A Escobedo
    posted to methodology free_energy expanded_ensemble by dmobley on 2008-06-23 20:09:06 as **
  • Accurate calculations of free-energy differences by the distribution method
    The Journal of Chemical Physics, Vol. 128, No. 22. (2008)
    by Di Wu
    posted to methodology free_energy by dmobley on 2008-06-16 16:10:24 as **
  • Are Current Molecular Dynamics Force Fields too Helical?
    Biophys. J., Vol. 95, No. 1. (1 July 2008), pp. L07-9.
    by Robert B Best, Nicolae-Viorel Buchete, Gerhard Hummer
    posted to no-tag by dmobley on 2008-06-12 17:40:18 as ** along with 1 person loison
  • Conformational entropy in molecular recognition by proteins
    Nature, Vol. 448, No. 7151., pp. 325-329.
    by Kendra K Frederick, Michael S Marlow, Kathleen G Valentine, Joshua A Wand
    posted to no-tag by dmobley on 2008-04-16 00:27:29 as ** along with 5 people zwang cactus Jporci jlh64 psique
  • Adaptive biasing force method for scalar and vector free energy calculations
    The Journal of Chemical Physics, Vol. 128, No. 14. (2008)
    by Eric Darve, David R Gómez, Andrew Pohorille
    posted to alchemical free_energy thermodynamic_integration by dmobley on 2008-04-15 00:38:27 as **
  • Adaptively biased molecular dynamics for free energy calculations
    The Journal of Chemical Physics, Vol. 128, No. 13. (2008)
    by Volodymyr Babin, Christopher Roland, Celeste Sagui
    posted to conformation free_energy by dmobley on 2008-04-09 22:50:36 as **
  • A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models
    The Journal of Chemical Physics, Vol. 128, No. 12. (2008)
    by Swaroop Chatterjee, Pablo G Debenedetti, Frank H Stillinger, Ruth
    posted to water by dmobley on 2008-04-05 16:28:31 as ** along with 1 person sunhwan
  • Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
    The Journal of Chemical Physics, Vol. 128, No. 11. (2008)
    by Yuqing Deng, Benoît Roux
    posted to binding free_energy grand_canonical by dmobley on 2008-03-21 21:01:44 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Calculation of free-energy differences and potentials of mean force by a multi-energy gap method
    The Journal of Chemical Physics, Vol. 128, No. 11. (2008)
    by Huan X Zhou
    posted to free_energy methodology by dmobley on 2008-03-21 20:58:23 as **
  • Benchmarking Implicit Solvent Folding Simulations of the Amyloid β(10-35) Fragment
    J. Phys. Chem. B (19 March 2008)
    by A Kent, AK Jha, JE Fitzgerald, KF Freed
    posted to amyloid implicit simulation by dmobley on 2008-03-21 20:46:33 as **
  • Molecular Modeling Based Approach to Potent P2-P4 Macrocyclic Inhibitors of Hepatitis C NS3/4A Protease
    J. Am. Chem. Soc. (14 March 2008)
    by NJ Liverton, MK Holloway, JA Mccauley, MT Rudd, JW Butcher, SS Carroll, J Dimuzio, C Fandozzi, KF Gilbert, SS Mao, CJ Mcintyre, KT Nguyen, JJ Romano, M Stahlhut, BL Wan, DB Olsen, JP Vacca
    posted to no-tag by dmobley on 2008-03-18 23:41:59 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 no-tag by dmobley on 2008-03-12 23:26:44 as ** along with 2 people kentsis daevans
  • Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design
    Biophys. J., Vol. 87, No. 5. (1 November 2004), pp. 3035-3049.
    by Wei Chen, Chia-En Chang, Michael K Gilson
    posted to no-tag by dmobley on 2008-03-12 23:24:59 as **
  • Concepts in Receptor Optimization: Targeting the RGD Peptide
    J. Am. Chem. Soc., Vol. 128, No. 14. (12 April 2006), pp. 4675-4684.
    by W Chen, Chang, MK Gilson
    posted to no-tag by dmobley on 2008-03-12 23:21:30 as **
  • Ligand configurational entropy and protein binding
    PNAS, Vol. 104, No. 5. (30 January 2007), pp. 1534-1539.
    by Chia-En A Chang, Wei Chen, Michael K Gilson
    posted to entropy by dmobley on 2008-03-12 23:11:06 as ** along with 1 person daevans
  • A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations
    The Journal of Chemical Physics, Vol. 128, No. 9. (2008)
    by Donghong Min, Wei Yang
    posted to no-tag by dmobley on 2008-03-07 21:15:33 as ****
  • Identification of the betaTP site in the x-ray structure of F1-ATPase as the high-affinity catalytic site
    Proceedings of the National Academy of Sciences, Vol. 104, No. 47. (20 November 2007), pp. 18478-18483.
    by Hui Z Mao, Joachim Weber
    posted to no-tag by dmobley on 2008-03-07 17:52:28 as ** along with 1 person cactus
  • Molecular mechanisms of resistance: Free energy calculations of mutation effects on inhibitor binding to HIV-1 protease
    Protein Sci, Vol. 7, No. 8. (1 August 1998), pp. 1750-1756.
    by SW Rick, IA Topol, JW Erickson, SK Burt
    posted to free_energy resistance by dmobley on 2008-03-06 22:03:16 as **
  • 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 free_energy water by dmobley on 2008-03-04 21:17:28 as ** along with 2 people jteyra daevans
  • Computational Study of the Mechanism and the Relative Free Energies of Binding of Anticholesteremic Inhibitors to Squalene-Hopene Cyclase
    Biochemistry, Vol. 47, No. 9. (4 March 2008), pp. 2945-2951.
    by Fabienne Schwab, Wilfred F Gunsteren, Bojan Zagrovic
    posted to alchemical free_energy by dmobley on 2008-03-04 20:37:44 as **
  • Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry
    J. Med. Chem. (24 January 2008)
    by Anthony Nicholls, David L Mobley, Peter J Guthrie, John D Chodera, Vijay S Pande
    posted to alchemical free_energy hydration by dmobley on 2008-03-04 18:35:13 as read along with 2 people and 1 group sobolevnrm middledomain baker-group
  • Charge Asymmetries in Hydration of Polar Solutes
    J. Phys. Chem. B (6 February 2008)
    by DL Mobley, AE Barber, CJ Fennell, KA Dill
    posted to alchemical free_energy hydration by dmobley on 2008-03-04 18:29:58 as read along with 3 people and 1 group sobolevnrm onufriev middledomain baker-group
  • Computational Study on the Structural Diversity of Amyloid Beta Peptide (Aβ10-35) Oligomers
    J. Phys. Chem. B (28 February 2008)
    by S Jang, S Shin
    posted to amyloid oligomers by dmobley on 2008-02-29 17:26:35 as ****
  • The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions
    Journal of Molecular Biology, Vol. 254, No. 5. (15 December 1995), pp. 801-807.
    by S Boresch, M Karplus
    posted to no-tag by dmobley on 2008-02-28 23:28:47 as ** along with 1 person Diego_Prada
  • Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations
    The Journal of Chemical Physics, Vol. 127, No. 21. (2007)
    by Thomas Steinbrecher, David L Mobley, David A Case
    posted to alchemical free_energy hydration by dmobley on 2008-02-28 22:03:08 as read along with 1 person and 1 group sobolevnrm baker-group
  • Calculation of the relative change in binding free energy of a protein-inhibitor complex.
    Science, Vol. 235, No. 4788. (30 January 1987), pp. 574-576.
    by PA Bash, UC Singh, FK Brown, R Langridge, PA Kollman
    posted to alchemical binding relative by dmobley on 2008-02-28 21:14:05 as ** along with 1 person apostola
  • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 673-685.
    by Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig
    posted to binding free_energy mmpbsa protonation by dmobley on 2008-02-27 17:26:21 as ** along with 2 people and 1 group sobolevnrm sunhwan baker-group
  • Fluoride-Selective Binding in a New Deep Cavity Calix[4]pyrrole: Experiment and Theory
    J. Am. Chem. Soc., Vol. 124, No. 29. (24 July 2002), pp. 8644-8652.
    by CJ Woods, S Camiolo, ME Light, SJ Coles, MB Hursthouse, MA King, PA Gale, JW Essex
    posted to alchemical binding free_energy by dmobley on 2008-02-27 00:20:34 as **
  • Antiviral drug design: computational analyses of the effects of the L100I mutation for HIV-RT on the binding of NNRTIs
    Bioorganic & Medicinal Chemistry Letters, Vol. 11, No. 21. (5 November 2001), pp. 2799-2802.
    by De-Ping Wang, Robert C Rizzo, Julian Tirado-Rives, William L Jorgensen
    posted to alchemical free_energy relative by dmobley on 2008-02-26 19:41:59 as **
  • Discovery of a Potent, Selective, and Efficacious Class of Reversible <img src="http://pubs.acs.org/images/gifchars/alpha.gif" border="0">-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase Effective as Analgesics
    J. Med. Chem., Vol. 48, No. 6. (24 March 2005), pp. 1849-1856.
    by DL Boger, H Miyauchi, W Du, C Hardouin, RA Fecik, H Cheng, I Hwang, MP Hedrick, D Leung, O Acevedo, CRW Guimaraes, WL Jorgensen, BF Cravatt
    posted to binding free_energy relative by dmobley on 2008-02-26 19:29:55 as **
  • Elucidation of Fatty Acid Amide Hydrolase Inhibition by Potent &#x03B1;-Ketoheterocycle Derivatives from Monte Carlo Simulations
    J. Am. Chem. Soc., Vol. 127, No. 49. (14 December 2005), pp. 17377-17384.
    by CRW Guimaraes, DL Boger, WL Jorgensen
    posted to binding free_energy relative by dmobley on 2008-02-26 19:27:06 as **
  • Assault on Resistance: The Use of Computational Chemistry in the Development of Anti-HIV Drugs
    Current Pharmaceutical Design, Vol. 12, No. 15. (May 2006), pp. 1843-1856.
    by Marilyn B Smith, Smith, William L Jorgensen
    posted to free_energy relative resistance review by dmobley on 2008-02-26 19:13:50 as **
  • Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein-Ligand Binding
    J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5880-5884.
    by J Tirado-Rives, WL Jorgensen
    posted to binding free_energy by dmobley on 2008-02-26 19:10:19 as ** along with 2 people daevans superpyrin
  • From Docking False-Positive to Active Anti-HIV Agent
    J. Med. Chem., Vol. 50, No. 22. (1 November 2007), pp. 5324-5329.
    by G Barreiro, JT Kim, CRW Guimaraes, CM Bailey, RA Domaoal, L Wang, KS Anderson, WL Jorgensen
    posted to binding hiv-rt mmpbsa by dmobley on 2008-02-26 19:05:21 as **
  • Search for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase Using Chemical Similarity, Molecular Docking, and MM-GB/SA Scoring
    J. Chem. Inf. Model., Vol. 47, No. 6. (26 November 2007), pp. 2416-2428.
    by G Barreiro, CRW Guimaraes, I Tubert-Brohman, TM Lyons, J Tirado-Rives, WL Jorgensen
    posted to binding mmpbsa by dmobley on 2008-02-26 19:05:00 as **
  • Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz
    Bioorganic & Medicinal Chemistry Letters, Vol. 18, No. 3. (1 February 2008), pp. 969-972.
    by Kroeger, Lenea H Rader, Amanda M Franklin, Emily V Taylor, Katie D Smith, Smith, Julian Tirado-Rives, William L Jorgensen
    posted to free_energy hiv-rt relative by dmobley on 2008-02-26 19:04:35 as **
  • Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens
    J. Med. Chem., Vol. 43, No. 24. (30 November 2000), pp. 4594-4605.
    by BC Oostenbrink, JW Pitera, MMH van Lipzig, JHN Meerman, WF van Gunsteren
    posted to binding free_energy relative by dmobley on 2008-02-26 18:42:26 as **
  • Induced Disorder in Protein-Ligand Complexes as a Drug-Design Strategy.
    Mol Pharm (16 February 2008)
    by Alejandro Crespo, Ariel Fernández
    posted to binding entropy free_energy by dmobley on 2008-02-26 18:17:58 as read along with 1 person higueruelo
  • Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation.
    J Med Chem, Vol. 48, No. 19. (22 September 2005), pp. 6117-6127.
    by PH Keizers, C de Graaf, FJ de Kanter, C Oostenbrink, KA Feenstra, JN Commandeur, NP Vermeulen
    posted to alchemical binding free_energy relative by dmobley on 2008-02-26 17:56:54 as ** along with 1 person feenstra
  • Molecular Modeling-Guided Site-Directed Mutagenesis of Cytochrome P450 2D6
    Current Drug Metabolism, Vol. 8, No. 1. (January 2007), pp. 59-77.
    by De Graaf, Chris, Oostenbrink, Chris, J Keizers, H Peter, A van Vugt-Lussenburg, M Barbara, B van Waterschoot, A Robert, Tschirret-Guth, A Richard, M Commandeur, N Jan, E Vermeulen, P Nico
    posted to alchemical free_energy relative by dmobley on 2008-02-26 00:35:32 as **
  • Identification of Critical Residues in Novel Drug Metabolizing Mutants of Cytochrome P450 BM3 Using Random Mutagenesis
    J. Med. Chem., Vol. 50, No. 3. (8 February 2007), pp. 455-461.
    by BMA Vanvugt-Lussenburg, E Stjernschantz, J Lastdrager, C Oostenbrink, PE Vermeulen, JNM Commandeur
    posted to binding free_energy relative by dmobley on 2008-02-25 22:28:04 as **
  • Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3
    Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 1. (2008), pp. 336-352.
    by Eva Stjernschantz, Barbara MA van Vugt-Lussenburg, Alois Bonifacio, Stephanie BA de Beer, Gert van der Zwan, Cees Gooijer, Jan NM Commandeur, Nico PE Vermeulen, Chris Oostenbrink
    posted to binding free_energy relative by dmobley on 2008-02-25 22:25:00 as ***
  • Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin-Streptavidin System Revisited
    J. Phys. Chem. A, Vol. 105, No. 42. (25 October 2001), pp. 9795-9799.
    by SB Dixit, C Chipot
    posted to absolute alchemical binding by dmobley on 2008-02-25 20:37:54 as ***
  • Conformational and Enantioselectivity in Host-Guest Chemistry: The Selective Binding of Cis Amides Examined by Free Energy Calculations
    J. Phys. Chem. B, Vol. 108, No. 45. (11 November 2004), pp. 17571-17582.
    by RH Henchman, JD Kilburn, DL Turner, JW Essex
    posted to binding free_energy relative by dmobley on 2008-02-25 18:27:29 as **
  • Proton Binding to Proteins: p<i>K</i><sub>a</sub> Calculations with Explicit and Implicit Solvent Models
    J. Am. Chem. Soc., Vol. 126, No. 13. (7 April 2004), pp. 4167-4180.
    by T Simonson, J Carlsson, DA Case
    posted to alchemical free_energy pka by dmobley on 2008-02-23 23:54:51 as *** along with 2 people and 1 group sobolevnrm RamuAnandakrishnan baker-group
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