Tag alchemical [32 articles] Export

Recent papers classified by the tag alchemical.

	Adaptive biasing force method for scalar and vector free energy calculations [My Copy] 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
	Computational Study of the Mechanism and the Relative Free Energies of Binding of Anticholesteremic Inhibitors to Squalene-Hopene Cyclase [My Copy] 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 [My Copy] 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 along with 2 people and 1 group sobolevnrm middledomain baker-group
	Charge asymmetries in hydration of polar solutes. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 8. (28 February 2008), pp. 2405-2414. by D. L. Mobley, A. E. Barber, C. J. Fennell, K. A. Dill posted to alchemical free_energy hydration by dmobley on 2008-03-04 18:29:58 as along with 4 people and 1 group flbarroso sobolevnrm onufriev middledomain baker-group
	Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations [My Copy] The Journal of Chemical Physics, Vol. 127, No. 21. (2007), 214108. 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 along with 3 people and 1 group sunnytov arnaucordomi sobolevnrm baker-group
	Calculation of the relative change in binding free energy of a protein-inhibitor complex. [My Copy] Science, Vol. 235, No. 4788. (30 January 1987), pp. 574-576. by P. A. Bash, U. C. Singh, F. K. Brown, R. Langridge, P. A. Kollman posted to alchemical binding relative by dmobley on 2008-02-28 21:14:05 as along with 1 person apostola
	Fluoride-Selective Binding in a New Deep Cavity Calix[4]pyrrole: Experiment and Theory [My Copy] J. Am. Chem. Soc., Vol. 124, No. 29. (24 July 2002), pp. 8644-8652. by C. J. Woods, S. Camiolo, M. E. Light, et al.S. J. Coles, M. B. Hursthouse, M. A. King, P. A. Gale, J. W. 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 [My Copy] 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
	Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation. [My Copy] J Med Chem, Vol. 48, No. 19. (22 September 2005), pp. 6117-6127. by P. H. Keizers, C. de Graaf, F. J. de Kanter, et al.C. Oostenbrink, K. A. Feenstra, J. N. Commandeur, N. P. 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 [My Copy] Current Drug Metabolism, Vol. 8, No. 1. (January 2007), pp. 59-77. by De Graaf, Chris, Oostenbrink, et al. 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
	Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin-Streptavidin System Revisited [My Copy] J. Phys. Chem. A, Vol. 105, No. 42. (25 October 2001), pp. 9795-9799. by S. B. Dixit, C. Chipot posted to absolute alchemical binding by dmobley on 2008-02-25 20:37:54 as
	Proton Binding to Proteins: pKa Calculations with Explicit and Implicit Solvent Models [My Copy] Journal of the American Chemical Society, Vol. 126, No. 13. (1 April 2004), pp. 4167-4180. by Thomas Simonson, Jens Carlsson, David A. Case posted to alchemical free_energy pka by dmobley on 2008-02-23 23:54:51 as along with 5 people and 1 group fralium flbarroso 6rheology sobolevnrm RamuAnandakrishnan baker-group
	Bornyl (3,4,5-trihydroxy)-cinnamate--an optimized human neutrophil elastase inhibitor designed by free energy calculations. [My Copy] Bioorganic & medicinal chemistry, Vol. 16, No. 5. (1 March 2008), pp. 2385-2390. 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 along with 1 person bmduggan
	MB06322 (CS-917): A potent and selective inhibitor of fructose 1,6-bisphosphatase for controlling gluconeogenesis in type 2 diabetes [My Copy] 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, et al.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 [My Copy] 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. [My Copy] J Comput Aided Mol Des, Vol. 17, No. 10. (October 2003), pp. 673-686. by A. Villa, R. Zangi, G. Pieffet, A. E. 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. [My Copy] J Am Chem Soc, Vol. 125, No. 35. (3 September 2003), pp. 10570-10579. by R. Talhout, A. Villa, A. E. Mark, J. B. Engberts posted to alchemical binding calorimetry free_energy by dmobley on 2008-02-23 02:07:13 as along with 1 person lillekatt
	Free Energy Simulations Come of Age: Protein−Ligand Recognition [My Copy] Accounts of Chemical Research, Vol. 35, No. 6. (1 June 2002), pp. 430-437. by Thomas Simonson, Georgios Archontis, Martin Karplus posted to alchemical free_energy relative by dmobley on 2008-02-22 22:18:59 as along with 2 people flbarroso dfgreen
	Rapid, Accurate, and Precise Calculation of Relative Binding Affinities for the SH2 Domain Using a Computational Grid [My Copy] J. Chem. Theory Comput., Vol. 3, No. 3. (8 May 2007), pp. 1193-1202. by P. W. Fowler, S. Geroult, S. Jha, G. Waksman, P. V. Coveney posted to alchemical free_energy by dmobley on 2008-02-19 00:53:50 as
	Prion and water: tight and dynamical hydration sites have a key role in structural stability. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 21. (24 May 2005), pp. 7535-7540. by A. De Simone, G. G. Dodson, C. S. Verma, A. Zagari, F. Fraternali posted to absolute alchemical free_energy water by dmobley on 2008-02-19 00:30:02 as along with 3 people scampos ffranca ashaytan
	The missing link between thermodynamics and structure in F1-ATPase [My Copy] Proceedings of the National Academy of Sciences, Vol. 100, No. 3. (4 February 2003), pp. 874-879. by W. Yang, Y. Q. Gao, Q. Cui, J. Ma, M. Karplus posted to alchemical relative by dmobley on 2008-01-26 01:46:23 as
	Optimization of replica exchange molecular dynamics by fast mimicking [My Copy] The Journal of Chemical Physics, Vol. 127, No. 20. (2007) by Jozef Hritz, Chris Oostenbrink posted to alchemical replica_exchange by dmobley on 2007-11-30 19:52:18 as
	The Rosicrucian Enlightenment (Routledge Classics) (Routledge Classics) [My Copy] (09 November 2001) by Frances A. Yates posted to alchemical andreae arts atlantis bacon bohemia britain bruno bry caus christian cross de dee dees elector elizabeth fama fludd forces francis general german giordano great hague inigo johann john jones king maier mathematical michael monas mouvantes movement new of palatine philosophy princess prints protestant queen reformation robert rose rosencreutz rosicrucian royal salomon satirical secret society the theatre theodore thirty tradition universal valentin war world years by lectorespa on 2007-11-01 21:20:14 as along with 1 person CUL_Akbar
	Determination of the Interfacial Water Content in Protein-Protein Complexes from Free Energy Simulations [My Copy] Biophys. J., Vol. 90, No. 3. (1 February 2006), pp. 841-850. by Peter Monecke, Thorsten Borosch, Jurgen Brickmann, Stefan M. Kast posted to alchemical binding free_energy methods water by dmobley on 2007-10-22 19:48:51 as
	Hydration Free Energies and Entropies for Water in Protein Interiors [My Copy] J. Am. Chem. Soc., Vol. 126, No. 25. (30 June 2004), pp. 7991-8000. by L. R. Olano, S. W. Rick posted to alchemical binding free_energy water by dmobley on 2007-10-22 19:46:27 as
	Hydrophilicity of cavities in proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 24, No. 4. (1996), pp. 433-438. by Li Zhang, Jan Hermans posted to alchemical binding free_energy water by dmobley on 2007-10-22 19:43:56 as
	A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins [My Copy] Biopolymers, Vol. 31, No. 8. (1991), pp. 919-931. by Rebecca C. Wade, Michael H. Mazor, Andrew J. Mccammon, Florante A. Quiocho posted to alchemical binding free_energy water by dmobley on 2007-10-22 19:42:24 as
	Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/Inhibitor Complexes [My Copy] J. Am. Chem. Soc., Vol. 128, No. 36. (13 September 2006), pp. 11830-11839. by Y. Lu, C. Y. Yang, S. Wang posted to alchemical binding free_energy water by dmobley on 2007-10-22 19:34:08 as along with 1 person ashaytan
	Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values [My Copy] Chemical Physics, Vol. 337, No. 1-3. (16 August 2007), pp. 135-143. by Yoshiaki Tanida, Masakatsu Ito, Hideaki Fujitani posted to absolute alchemical free_energy by dmobley on 2007-10-22 17:32:49 as
	Binding Free Energies and Free Energy Components from Molecular Dynamics and Poisson-Boltzmann Calculations. Application to Amino Acid Recognition by Aspartyl-tRNA Synthetase [My Copy] pp. 307-327. by G. Archontis posted to alchemical free_energy by dmobley on 2007-10-19 01:37:39 as
	Biased Sampling of Nonequilibrium Trajectories: Can Fast Switching Simulations Outperform Conventional Free Energy Calculation Methods? [My Copy] J. Phys. Chem. B, Vol. 109, No. 14. (14 April 2005), pp. 6902-6915. by H. Oberhofer, C. Dellago, P. L. Geissler posted to alchemical free_energy jarzynski by dmobley on 2007-10-19 00:48:49 as
	Predicting Absolute Ligand Binding Free Energies to a Simple Model Site [My Copy] 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 alchemical binding free_energy simulation by dmobley on 2007-10-18 23:12:57 as along with 6 people and 3 groups allmensch oteri barry insilico daevans superpyrin structural_bioinformatics Bioinformatics Computer Aided Drug Design

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free_energy	27
binding	11
relative	7
water	7
absolute	3
hydration	3
andreae	1
arts	1
atlantis	1
bacon	1
bohemia	1
britain	1
bruno	1
bry	1
calorimetry	1
caus	1
christian	1
cross	1
de	1
dee	1
dees	1
elector	1
elizabeth	1
fama	1
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forces	1
francis	1
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inigo	1
jarzynski	1
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maier	1
mathematical	1
methods	1
michael	1
monas	1
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movement	1
new	1
of	1
palatine	1
philosophy	1
pka	1
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prints	1
protestant	1
queen	1
reformation	1
replica_exchange	1
robert	1
rose	1
rosencreutz	1
rosicrucian	1
royal	1
salomon	1
satirical	1
secret	1
simulation	1
society	1
theatre	1
theodore	1
thermodynamic_integration	1
thirty	1
tradition	1
universal	1
valentin	1
war	1
world	1
years	1

Tag alchemical [32 articles] Export

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