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dmobley free_energy [91 articles]

最近 dmobley さんのライブラリに追加された論文の中から タグ free_energy. You can also see everyone's free_energy.
  • Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
    J. Chem. Theory Comput. (13 August 2008)
    by César A de Oliveira, Donald Hamelberg, Andrew J Mccammon
    posted to ti free_energy accelerated_md by dmobley on 2008-08-15 19:51:40 as **** along with 1 person and 1 group cesar McCammon
  • Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State
    J. Chem. Theory Comput. (13 August 2008)
    by Ilja V Khavrutskii, Mikolai Fajer, Andrew J Mccammon
    posted to free_energy conformation by dmobley on 2008-08-15 19:50:48 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 **
  • 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 **
  • 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 **
  • 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 3 people LamBras 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
  • 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
  • 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 3 people and 1 group boris_aguilar 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
  • 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 ***
  • 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
  • Bornyl (3,4,5-trihydroxy)-cinnamate - An optimized human neutrophil elastase inhibitor designed by free energy calculations
    Bioorganic & Medicinal Chemistry, Vol. In Press, Corrected Proof
    by Thomas Steinbrecher, Andrea Hrenn, Korinna L Dormann, Irmgard Merfort, Andreas Labahn
    posted to alchemical free_energy relative by dmobley on 2008-02-23 23:48:12 as ***
  • MB06322 (CS-917): A potent and selective inhibitor of fructose 1,6-bisphosphatase for controlling gluconeogenesis in type 2 diabetes
    Proceedings of the National Academy of Sciences, Vol. 102, No. 22. (31 May 2005), pp. 7970-7975.
    by Mark D Erion, Paul D van Poelje, Qun Dang, Srinivas R Kasibhatla, Scott C Potter, Rami M Reddy, Raja K Reddy, Tao Jiang, William N Lipscomb
    posted to alchemical free_energy by dmobley on 2008-02-23 22:02:17 as **
  • Hydration energy landscape of the active site cavity in cytochrome P450cam
    Proteins: Structure, Function, and Genetics, Vol. 32, No. 3. (1998), pp. 381-396.
    by Volkhard Helms, Rebecca C Wade
    posted to alchemical free_energy water by dmobley on 2008-02-23 21:52:14 as **
  • Sampling and convergence in free energy calculations of protein-ligand interactions: the binding of triphenoxypyridine derivatives to factor Xa and trypsin.
    J Comput Aided Mol Des, Vol. 17, No. 10. (October 2003), pp. 673-686.
    by A Villa, R Zangi, G Pieffet, AE Mark
    posted to alchemical free_energy by dmobley on 2008-02-23 02:12:30 as **
  • Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin.
    J Am Chem Soc, Vol. 125, No. 35. (3 September 2003), pp. 10570-10579.
    by R Talhout, A Villa, AE Mark, JB Engberts
    posted to alchemical binding calorimetry free_energy by dmobley on 2008-02-23 02:07:13 as *** along with 1 person lillekatt
  • Calculation of the Redox Potential of the Protein Azurin and Some Mutants
    ChemBioChem, Vol. 6, No. 4. (2005), pp. 738-746.
    by Marieke van den Bosch, Marcel Swart, Jaap G Snijders?, Herman JC Berendsen, Alan E Mark, Chris Oostenbrink, Wilfred F van Gunsteren, Gerard W Canters
    posted to alchemiccal free_energy relative by dmobley on 2008-02-23 01:10:21 as read
  • Free Energy Simulations Come of Age: Protein-Ligand Recognition
    Acc. Chem. Res., Vol. 35, No. 6. (18 June 2002), pp. 430-437.
    by T Simonson, G Archontis, M Karplus
    posted to alchemical free_energy relative by dmobley on 2008-02-22 22:18:59 as **
  • Ligand Binding to the Voltage-Gated Kv1.5 Potassium Channel in the Open State Docking and Computer Simulations of a Homology Model
    Biophys. J., Vol. 94, No. 3. (1 February 2008), pp. 820-831.
    by Martin Ander, Victor B Luzhkov, Johan Aqvist
    posted to free_energy lie by dmobley on 2008-02-22 21:48:50 as **
  • Computation of Free Energy
    Helvetica Chimica Acta, Vol. 85, No. 10. (2002), pp. 3113-3129.
    by Wilfred f, Xavier Daura, Alan e
    posted to free_energy relative review by dmobley on 2008-02-22 19:03:07 as ***
  • Proline cis-trans isomerization in staphylococcal nuclease: Multi-substate free energy perturbation calculations
    Protein Sci, Vol. 4, No. 4. (1 April 1995), pp. 636-654.
    by A Hodel, LM Rice, T Simonson, RO Fox, AT Brunger
    posted to conformation free_energy by dmobley on 2008-02-22 18:37:02 as ****
  • Finding Transition Pathways Using the String Method with Swarms of Trajectories
    J. Phys. Chem. B (22 February 2008)
    by AC Pan, D Sezer, B Roux
    posted to conformation free_energy methodology by dmobley on 2008-02-22 16:01:27 as *** along with 1 person and 1 group sobolevnrm baker-group
  • Molecular evolution of affinity and flexibility in the immune system
    Proceedings of the National Academy of Sciences, Vol. 104, No. 21. (22 May 2007), pp. 8821-8826.
    by Ian F Thorpe, Charles L Brooks
    posted to free_energy mmpbsa by dmobley on 2008-02-19 01:17:47 as **
  • Rapid, Accurate, and Precise Calculation of Relative Binding Affinities for the SH2 Domain Using a Computational Grid
    J. Chem. Theory Comput., Vol. 3, No. 3. (8 May 2007), pp. 1193-1202.
    by PW Fowler, S Geroult, S Jha, G Waksman, PV Coveney
    posted to alchemical free_energy by dmobley on 2008-02-19 00:53:50 as **
  • Molecular Basis of Peptide Recognition by the TCR: Affinity Differences Calculated Using Large Scale Computing
    J Immunol, Vol. 175, No. 3. (1 August 2005), pp. 1715-1723.
    by Shunzhou Wan, Peter V Coveney, Darren R Flower
    posted to free_energy by dmobley on 2008-02-19 00:53:04 as **
  • Prion and water: tight and dynamical hydration sites have a key role in structural stability.
    Proc Natl Acad Sci U S A, Vol. 102, No. 21. (24 May 2005), pp. 7535-7540.
    by A De Simone, GG Dodson, CS Verma, A Zagari, F Fraternali
    posted to absolute alchemical free_energy water by dmobley on 2008-02-19 00:30:02 as *** along with 2 people ffranca ashaytan
  • The self-referential method combined with thermodynamic integration
    The Journal of Chemical Physics, Vol. 128, No. 6. (2008)
    by Martin B Sweatman, Alexander A Atamas, Jean M Leyssale
    posted to free_energy solubility by dmobley on 2008-02-15 16:02:59 as ***
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