vahmurk's qmmm [30 articles] Export

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	Structural and energetic determinants of primary proton transfer in bacteriorhodopsin [My Copy] Photochem. Photobiol. Sci., Vol. 5, No. 6. (2006), pp. 547-552. by Ana-Nicoleta Bondar, Jeremy C. Smith, Stefan Fischer posted to back_isomerisation bacteriorhodopsin proton_pathways qmmm by vahmurk on 2009-02-08 23:06:11 as
	Three-Layer ONIOM Studies of the Dark State of Rhodopsin: The Protonation State of Glu181 [My Copy] Journal of Molecular Biology, Vol. 383, No. 1. (31 October 2008), pp. 106-121. by K. Hall, T. Vreven, M. Frisch, M. Bearpark posted to 081218 qmmm rhodopsin spectrum by vahmurk on 2008-12-17 22:13:10 as
	Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package. [My Copy] J Phys Chem A (24 May 2007) by Gustavo D. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg posted to 081218 bacteriorhodopsin mechanism qmmm by vahmurk on 2008-12-17 22:11:05 as along with 3 people and 1 group krapnik charris5 xdeupi LabCompMed
	<i>Ab initio</i>, tight-binding and QM/MM calculations of the rhodopsin chromophore in its binding pocket [My Copy] Phase Transitions, Vol. 77, No. 1. (2004), pp. 31-45. by M. Sugihara, V. Buss, P. Entel, et al.J. Hafner, A. N. Bondar, M. Elstner, T. Frauenheim posted to 081218 md photoisomeration protein qm qmmm rhodopsin spectrum water by vahmurk on 2008-12-17 21:34:39 as
	Structures and spectral signatures of protonated water networks in bacteriorhodopsin. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 6980-6985. by G. Mathias, D. Marx posted to 081207 bacteriorhodopsin cpmd qmmm water by vahmurk on 2008-12-07 10:51:14 as along with 2 people and 1 group xdeupi saravan LabCompMed
	Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints [My Copy] Journal of Computational Chemistry, Vol. 24, No. 6. (2003), pp. 760-769. by Thom Vreven, Keiji Morokuma, Ödön Farkas, Bernhard H. Schlegel, Michael J. Frisch posted to 081118 bacteriorhodopsin method qmmm retinal spectrum uv by vahmurk on 2008-11-17 23:45:03 as
	Investigation of the S0S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid method [My Copy] Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), Vol. 109, No. 3. (18 April 2003), pp. 125-132. by T. Vreven, K. Morokuma posted to 081118 bacteriorhodopsin method opsin_shift qmmm retinal spectrum uv by vahmurk on 2008-11-17 23:40:25 as
	Mechanism of color tuning in retinal protein: SAC-CI and QM/MM study [My Copy] Chemical Physics Letters, Vol. 414, No. 1-3. (03 October 2005), pp. 239-242. by K. Fujimoto, J. Hasegawa, S. Hayashi, S. Kato, H. Nakatsuji posted to 081002 bacteriorhodopsin light_absorption mechanism photoisomeration pigments qmmm retinal spectrum by vahmurk on 2008-10-02 21:45:04 as
	Effects of the protein electrostatic environment on the absorption maximum of bacteriorhodopsin [My Copy] Chemical Physics Letters, Vol. 294, No. 1-3. (11 September 1998), pp. 162-166. by H. Houjou posted to 081002 bacteriorhodopsin light_absorption qmmm spectrum by vahmurk on 2008-10-02 21:23:42 as
	Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event [My Copy] The Journal of Physical Chemistry B, Vol. 105, No. 40. (1 October 2001), pp. 9857-9871. by A. Warshel, Z. T. Chu posted to bacteriorhodopsin light_absorption md mechanism photoisomeration qmmm by vahmurk on 2008-09-28 10:23:44 as along with 1 person katarzinia
	Photoexcited breathers in conjugated polyenes: An excited-state molecular dynamics study [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 5. (4 March 2003), pp. 2185-2190. by S. Tretiak, A. Saxena, R. L. Martin, A. R. Bishop posted to md method polyenes qmmm by vahmurk on 2008-09-28 10:21:57 as
	The role of intersection topography in bond selectivity of cis-trans photoisomerization [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 4. (19 February 2002), pp. 1769-1773. by M. Ben-Nun, F. Molnar, K. Schulten, Todd J. Martínez posted to photoisomeration qmmm retinal structure by vahmurk on 2008-09-28 10:16:21 as
	Computational evidence in favor of a two-state, two-mode model of the retinal chromophore photoisomerization [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 17. (2000), pp. 9379-9384. by Remedios González-Luque, Marco Garavelli, Fernando Bernardi, Manuela Merchán, Michael A. Robb, Massimo Olivucci posted to mechanism membrane photoisomeration qmmm retinal by vahmurk on 2008-09-28 10:08:13 as
	Proton Transfer in Bacteriorhodopsin: Structure, Excitation, IR Spectra, and Potential Energy Surface Analyses by an ab Initio QM/MM Method [My Copy] J. Phys. Chem. B, Vol. 104, No. 45. (16 November 2000), pp. 10678-10691. by S. Hayashi, I. Ohmine posted to 081006 bacteriorhodopsin gpcr protein proton_pathways qmmm spectrum by vahmurk on 2008-09-28 10:07:02 as
	Study on the prediction of visible absorption maxima of azobenzene compounds. [My Copy] Journal of Zhejiang University. Science. B, Vol. 6, No. 6. (June 2005), pp. 584-589. by J. N. Liu, Z. R. Chen, S. F. Yuan posted to method qmmm by vahmurk on 2008-09-27 00:23:56 as
	Flexible effective fragment QM/MM method: validation through the challenging tests. [My Copy] Journal of computational chemistry, Vol. 24, No. 12. (September 2003), pp. 1410-1420. by A. V. Nemukhin, B. L. Grigorenko, I. A. Topol, S. K. Burt posted to method qmmm by vahmurk on 2008-09-27 00:20:58 as
	Computational analysis of the proton translocation from Asp96 to schiff base in bacteriorhodopsin. [My Copy] The journal of physical chemistry. B, Vol. 110, No. 45. (16 November 2006), pp. 22804-22812. by Y. Sato, M. Hata, S. Neya, T. Hoshino posted to bacteriorhodopsin gpcr isomerisation md mechanism proton_pathways qmmm retinal by vahmurk on 2008-09-27 00:17:11 as
	An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase. [My Copy] Journal of the American Chemical Society, Vol. 129, No. 43. (31 October 2007), pp. 13035-13042. by K. Bravaya, A. Bochenkova, A. Granovsky, A. Nemukhin posted to gpcr md opsin_shift qmmm retinal rhodopsin by vahmurk on 2008-09-27 00:09:09 as
	QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. [My Copy] Biophysical journal, Vol. 87, No. 5. (November 2004), pp. 2931-2941. by J. A. Gascon, V. S. Batista posted to 081006 bacteriorhodopsin md mechanism qmmm retinal rhodopsin vision by vahmurk on 2008-09-27 00:06:20 as
	Hybrid molecular dynamics-quantum mechanics simulations of solute spectral properties in the condensed phase: evaluation of simulation parameters. [My Copy] Journal of computational chemistry, Vol. 28, No. 9. (15 July 2007), pp. 1572-1581. by M. C. Zwier, J. M. Shorb, B. P. Krueger posted to method qmmm spectrum by vahmurk on 2008-09-26 23:57:43 as
	Absorption of schiff-base retinal chromophores in vacuo. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 35. (7 September 2005), pp. 12347-12350. by L. H. Andersen, I. B. Nielsen, M. B. Kristensen, et al.M. O. El Ghazaly, S. Haacke, M. B. Nielsen, M. A. Petersen posted to light_absorption md method qmmm retinal spectrum by vahmurk on 2008-09-26 23:57:07 as
	Calculating absorption shifts for retinal proteins: computational challenges. [My Copy] The journal of physical chemistry. B, Vol. 109, No. 8. (3 March 2005), pp. 3606-3615. by M. Wanko, M. Hoffmann, P. Strodel, et al.A. Koslowski, W. Thiel, F. Neese, T. Frauenheim, M. Elstner posted to method protein qmmm retinal by vahmurk on 2008-09-26 23:55:34 as
	Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method [My Copy] Journal of Computational Chemistry, Vol. 27, No. 14. (2006), pp. 1623-1630. by Azuma Matsuura, Hiroyuki Sato, Hirohiko Houjou, Shino Saito, Tomohiko Hayashi, Minoru Sakurai posted to bacteriorhodopsin gpcr md method pigments prediction protein qmmm rhodopsin spectrum structure by vahmurk on 2008-09-26 23:47:03 as
	On the color-tuning mechanism of Human-Blue visual pigment: SAC-CI and QM/MM study [My Copy] Chemical Physics Letters, Vol. 432, No. 1-3. (4 December 2006), pp. 252-256. by Kazuhiro Fujimoto, Jun-Ya Hasegawa, Shigehiko Hayashi, Hiroshi Nakatsuji posted to pigments protein qmmm rhodopsin structure vision by vahmurk on 2008-09-16 23:10:43 as
	Computational photochemistry of retinal proteins. [My Copy] Journal of computer-aided molecular design, Vol. 20, No. 7-8. (g 2006), pp. 511-518. by M. Wanko, M. Hoffmann, T. Frauenheim, M. Elstner posted to gpcr md protein qmmm rhodopsin spectrum structure by vahmurk on 2008-09-16 23:09:25 as
	Exploring the Molecular Mechanism for Color Distinction in Humans [My Copy] J. Phys. Chem. B, Vol. 110, No. 34. (31 August 2006), pp. 17230-17239. by R. J. Trabanino, N. Vaidehi, W. A. Goddard posted to gpcr md membrane protein qmmm rhodopsin by vahmurk on 2008-09-16 23:08:46 as
	Rhodopsin and GFP Chromophores: QM/MM Absorption Spectra in Solvent and Protein [My Copy] AIP Conf. Proc., Vol. 963, No. 2. (26 December 2007), pp. 689-692. by Piero Altoè, Marco Stenta, Marco Garavellia posted to gpcr md membrane protein qmmm rhodopsin spectrum structure by vahmurk on 2008-09-16 23:04:12 as
	Retinal Photoisomerization in Rhodopsin: Electrostatic and Steric Catalysis [My Copy] AIP Conference Proceedings, Vol. 963, No. 2. (2007), pp. 727-730. by Gaia Tomasello, Piero Altoè, Marco Stenta, Gloria O. González, Marco Garavelli, Giorgio Orlandi edited by Theodore E. Simos, George Maroulis posted to gpcr md photoisomeration protein qmmm rhodopsin structure by vahmurk on 2008-09-16 23:00:37 as
	Computational studies of the primary phototransduction event in visual rhodopsin. [My Copy] Accounts of chemical research, Vol. 39, No. 3. (March 2006), pp. 184-193. by J. A. Gascón, E. M. Sproviero, V. S. Batista posted to gpcr qmmm rhodopsin structure by vahmurk on 2008-09-16 22:59:38 as
	Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 22. (5 June 2008), pp. 6814-6827. by A. Altun, S. Yokoyama, K. Morokuma posted to md qmmm rhodopsin by vahmurk on 2008-09-16 11:30:47 as

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bacteriorhodopsin	73
structure	44
protein	34
mechanism	34
gpcr	34
retinal	32
qmmm	30
md	30
photoisomeration	30
rhodopsin	29
membrane	25
spectrum	24
proton_pathways	24
light_absorption	17
photocycle	17
pigments	16
081002	16
review	16
081006	14
method	13
isomerisation	13
lipid-bilayer	12
vision	9
conformational_changes	8
mutation	8
water	7
signal-transduction	5
uv	5
excited_state	5
prediction	5
081218	5
optical_disc	4
schiff_base	4
trimer	3
nanotechnology	3
channel	3
opsin_shift	3
back_isomerisation	2
081118	2
090405	2
switch	2
charges	2
monomer	2
qm	2
n	1
channels	1
081207	1
environment_support	1
j-625	1
adaptation	1
090105	1
cpmd	1
electrostatic_interactions	1
free_energy	1
autoisomerisation	1
of	1
dimer	1
gramicidin	1
l	1
protein-retinal_coupling	1
polyenes	1
namd	1
m	1

vahmurk's qmmm [30 articles] Export

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