xdeupi's md [35 articles] Export

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	Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. [My Copy] Journal of molecular modeling, Vol. 15, No. 8. (August 2009), pp. 959-969. by Saravana Prakash P. Thirumuruganandham, Herbert M. Urbassek posted to membrane_proteins md flexibility energy_landscape dynamics disorder by xdeupi on 2009-10-25 11:22:15 as along with 2 people saravan gcaltabiano
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted to review md by xdeupi on 2009-10-08 11:13:56 as along with 11 people and 1 group agrossfield allmensch bmduggan r2s2 apaydin kiekyon Borelli idoerg sobolevnrm edws paulschlesinger baker-group
	Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 12. (24 March 2009), pp. 4689-4694. by Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, David E. Shaw posted to theory structure modeling md flexibility dynamics b2ar activation by xdeupi on 2009-10-08 11:13:04 as along with 2 people dimka agrossfield
	Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists. [My Copy] Proteins (12 August 2009) by Brajesh K. Rai, Gregory J. Tawa, Alan H. Katz, Christine Humblet posted to theory modeling md gpcr by xdeupi on 2009-10-06 19:31:07 as
	Exploring Molecular Mechanisms of Ligand Recognition by Opioid Receptors with Metadynamics. [My Copy] Biochemistry (28 September 2009) by Davide Provasi, Andrea Bortolato, Marta Filizola posted to pathways md binding_kinetics binding by xdeupi on 2009-10-06 19:30:24 as
	Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. [My Copy] Proteins, Vol. 76, No. 2. (1 August 2009), pp. 403-417. by George Khelashvili, Alan Grossfield, Scott E. Feller, Michael C. Pitman, Harel Weinstein posted to theory rhodopsin md cholesterol by xdeupi on 2009-10-06 18:06:55 as along with 1 person and 1 group sobolevnrm baker-group
	Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies [My Copy] Journal of Molecular Modeling by Gilles Pieffet, Pavel Petukhov posted to theory spectroscopy modeling md fluorescence amber by xdeupi on 2009-09-15 14:25:43 as
	Chaos in Biomolecular Dynamics [My Copy] J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8101-8105. by H. Zhou, L. Wang posted to dynamics folding md modeling theory by xdeupi on 2009-06-08 12:28:13 as along with 1 person allmensch
	Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. [My Copy] Biochemistry (20 April 2009) by Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger posted to activation b2ar dry dynamics flexibility ionic lock md protonation solvation switch tm3 tm6 water by xdeupi on 2009-05-06 09:56:27 as along with 3 people and 1 group arnaucordomi jmccammon agrossfield McCammon
	Protein Dynamics, Thermal Stability, and Free-Energy Landscapes: A Molecular Dynamics Investigation [My Copy] Vol. 85, No. 4. (1 October 2003), pp. 2641-2649. by Ivano Tavernelli, Simona Cotesta, Ernesto E. Di Iorio posted to activation dynamics flexibility md nmr ser by xdeupi on 2009-03-16 20:05:04 as
	Development and testing of a general amber force field. [My Copy] J Comput Chem, Vol. 25, No. 9. (15 July 2004), pp. 1157-1174. by J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case posted to amber dynamics md theory by xdeupi on 2007-06-26 13:51:26 as along with 10 people and 1 group rdf paddydu nigham lillekatt gane5h kazemi megs easybakemuffin AndreaColetta pavanghatty LabCompMed
	Performance of the general amber force field in modeling aqueous POPC membrane bilayers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058. by Balázs Jójárt, Tamás A. Martinek posted to amber dynamics md membrane modeling theory by xdeupi on 2007-06-26 13:32:45 as along with 3 people and 1 group dimka easybakemuffin viktor21614 LabCompMed
	Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. [My Copy] J Comput Chem (31 January 2007) by Arnau Cordomí, Olle Edholm, Juan J J. Perez posted to dynamics md membrane rhodopsin theory by xdeupi on 2007-06-25 10:30:55 as along with 2 people and 1 group patricia arnaucordomi LabCompMed
	An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies [My Copy] Protein Eng., Vol. 9, No. 11. (1996), pp. 1063-1065. by Lawrence A. Kelley, Stephen P. Gardner, Michael J. Sutcliffe posted to dynamics helix md modeling structure theory by xdeupi on 2007-05-31 10:31:28 as along with 1 group LabCompMed
	Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin. [My Copy] J Am Chem Soc (15 May 2007) by Ting Wang, Yong Duan posted to activation agonist amber binding ligands md modeling rhodopsin by xdeupi on 2007-05-21 10:04:04 as along with 1 group LabCompMed
	Protein flexibility using constraints from molecular dynamics simulations. [My Copy] Phys Biol, Vol. 2, No. 4. (November 2005) by T. Mamonova, B. Hespenheide, R. Straub, M. F. Thorpe, M. Kurnikova posted to activation dynamics flexibility md by xdeupi on 2007-05-21 09:38:21 as along with 3 people and 1 group lna LamBras higueruelo LabCompMed
	Modeling activated states of GPCRs: the rhodopsin template. [My Copy] J Comput Aided Mol Des, Vol. 20, No. 7-8. (g 2006), pp. 437-448. by M. Y. Niv, L. Skrabanek, M. Filizola, H. Weinstein posted to activation dynamics md rhodopsin by xdeupi on 2007-03-26 10:22:13 as along with 1 person and 1 group IrinaMoreira LabCompMed
	Setting up and running molecular dynamics simulations of membrane proteins. [My Copy] Methods (San Diego, Calif.), Vol. 41, No. 4. (April 2007), pp. 475-488. by Christian Kandt, Walter L. Ash, D. Peter Tieleman posted to dynamics md membrane modeling review transmembrane by xdeupi on 2007-03-26 10:15:17 as along with 3 people and 2 groups arnaucordomi choonpeng sobolevnrm LabCompMed baker-group
	Molecular dynamics simulation of the human adenosine A3 receptor: agonist induced conformational changes of Trp243 [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 10-11. (October 2006), pp. 673-684. by Hallmen, Christian, Wiese, Michael posted to dynamics lipids md membrane by xdeupi on 2007-03-12 14:22:10 as along with 1 group LabCompMed
	How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. [My Copy] Proteins, Vol. 66, No. 3. (15 February 2007), pp. 559-574. by P. S. Crozier, M. J. Stevens, T. B. Woolf posted to activation dynamics md modeling rhodopsin switch by xdeupi on 2007-02-26 09:15:15 as along with 1 group LabCompMed
	A methyl group at C7 of 11-cis-retinal allows chromophore formation but affects rhodopsin activation. [My Copy] Vision Res (5 October 2006) by Laia Bosch, Arnau Cordomí, Marta Domínguez, et al.Darwin Toledo, Margarita Morillo, Juan J J. Pérez, Rosana Alvarez, Angel R R. de Lera, Pere Garriga posted to activation dynamics md rhodopsin by xdeupi on 2007-02-20 09:56:24 as along with 1 person and 1 group arnaucordomi LabCompMed
	Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. [My Copy] J Comput Aided Mol Des (7 November 2006) by Marta Filizola, Simon X. Wang, Harel Weinstein posted to activation dynamics gpcr lipids md membrane rhodopsin structure by xdeupi on 2006-11-14 16:42:29 as along with 1 group LabCompMed
	A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations. [My Copy] Biophys J, Vol. 91, No. 7. (1 October 2006), pp. 2647-2664. by C. Beier, H. J. Steinhoff posted to dynamics loops md modeling spin_labeling structure by xdeupi on 2006-10-30 18:37:07 as along with 1 group LabCompMed
	dummy [My Copy] by Dummy posted to 5ht1a activation agonist amber amine arrestin b2ar bimane binding cam ccr5 channel chemokine chimera crystallography cterm cxcr1 d250 dimer disease drug dry dynamics ecl2 evolution expression fluorescence folding fret genome gly gpcr gproteins hbond helix helix8 histamine hormone icl3 imaging internalization ionic leukotriene lhr ligands lipids lock loops md membrane modeling mutation n745 n749 nmr npxxy nterm opioid pharmacology polymorphism pro-kink protonation review rhodopsin s542 sequence ser spin_labeling structure switch thr thyrotropin tm2 tm3 tm5 tm6 tm7 toggle transmembrane trp txp w648 by xdeupi on 2006-10-30 12:30:16 as along with 2 people and 1 group jessicaopacic ivanrt LabCompMed
	Asymmetric stability among the transmembrane helices of lactose permease. [My Copy] Biochemistry, Vol. 45, No. 26. (4 July 2006), pp. 8088-8095. by M. Bennett, R. D'Rozario, M. S. Sansom, P. L. Yeagle posted to activation dynamics helix md modeling structure transmembrane by xdeupi on 2006-09-05 11:09:02 as along with 1 group LabCompMed
	TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations [My Copy] Journal of Computer-Aided Molecular Design, Vol. 20, No. 2. (February 2006), pp. 97-107. by Mezei, Mihaly, Filizola, Marta posted to md modeling structure transmembrane by xdeupi on 2006-07-21 12:20:38 as along with 1 group LabCompMed
	The role of extra-membranous inter-helical loops in helix-helix interactions. [My Copy] Protein Eng Des Sel, Vol. 18, No. 12. (December 2005), pp. 563-570. by M. B. Ulmschneider, D. P. Tieleman, M. S. Sansom posted to dynamics helix loops md membrane transmembrane by xdeupi on 2006-03-06 09:46:32 as along with 2 people and 1 group thaliana allanlo LabCompMed
	Conformational dynamics of M2 helices in KirBac channels: helix flexibility in relation to gating via molecular dynamics simulations. [My Copy] Biochemistry, Vol. 44, No. 44. (8 November 2005), pp. 14586-14594. by A. Grottesi, C. Domene, B. Hall, M. S. Sansom posted to activation channel dynamics md membrane modeling transmembrane by xdeupi on 2006-02-20 09:24:41 as along with 1 person and 1 group dimka LabCompMed
	Automatic atom type and bond type perception in molecular mechanical calculations. [My Copy] J Mol Graph Model (1 February 2006) by Junmei Wang, Wei Wang, Peter A A. Kollman, David A A. Case posted to amber dynamics md modeling by xdeupi on 2006-02-13 15:46:26 as along with 5 people and 1 group A_Coletta_Thesis dgruiz nigham marcvanhouteghem AndreaColetta LabCompMed
	A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [My Copy] Journal of Computational Chemistry, Vol. 24, No. 16. (December 2003), pp. 1999-2012. by Yong Duan, Chun Wu, Shibasish Chowdhury, et al.Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman posted to amber dynamics md modeling by xdeupi on 2006-01-24 11:35:18 as along with 6 people and 1 group Vadikus flbarroso ashaytan Lombardo_7 A_Coletta_Thesis schlauchi LabCompMed
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by David A. Case, Thomas E. Cheatham, Tom Darden, et al.Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods posted to amber md by xdeupi on 2006-01-20 09:35:28 as along with 18 people and 3 groups krapnik csrocha nickolay mmuecke flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	Molecular dynamics simulation of a phosphatidylglycerol membrane. [My Copy] FEBS Lett (6 December 2005) by Donald E E. Elmore posted to lipids md by xdeupi on 2006-01-13 10:20:29 as along with 3 people and 4 groups dimka piscinero softsimu Fluid-Mechanics-and-Thermal-Science-Research Computational_Systems_Biology XMLDataManagement LabCompMed
	Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments. [My Copy] J Mol Model (Online) (25 October 2005), pp. 1-16. by Birgit Schlegel, Wolfgang Sippl, Hans-Dieter D. Höltje posted to md membrane rhodopsin by xdeupi on 2005-11-04 22:46:37 as along with 1 person and 1 group saravan LabCompMed
	Molecular simulations and lipid-protein interactions: potassium channels and other membrane proteins. [My Copy] Biochem Soc Trans, Vol. 33, No. Pt 5. (October 2005), pp. 916-920. by M. S. Sansom, P. J. Bond, S. S. Deol, A. Grottesi, S. Haider, Z. A. Sands posted to gpcr md membrane by xdeupi on 2005-11-04 22:45:26 as along with 1 person and 1 group dimka LabCompMed
	Influence of the environment in the conformation of alpha-helices studied by protein database search and molecular dynamics simulations. [My Copy] Biophysical journal, Vol. 82, No. 6. (June 2002), pp. 3207-3213. by M. Olivella, X. Deupi, C. Govaerts, L. Pardo posted to helix md by xdeupi on 2005-10-25 03:17:23 as along with 2 people and 1 group carlosjavierna choonpeng LabCompMed

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activation	173
gpcr	112
structure	89
rhodopsin	79
review	65
modeling	62
b2ar	58
dynamics	56
helix	50
transmembrane	47
agonist	46
binding	45
theory	44
ligands	41
drug	36
md	35
switch	34
membrane_proteins	31
pharmacology	31
crystallography	30
nmr	30
membrane	26
gproteins	24
dimer	20
fluorescence	18
sequence	17
ser	17
active-state	15
pro-kink	15
folding	14
fret	14
genome	14
loops	14
flexibility	13
disease	12
tm6	12
cterm	11
mutation	11
retinal	11
amber	10
energy_landscape	10
evolution	10
toggle	10
arrestin	9
docking	9
kinetics	9
lipids	9
neurokinin	9
tm5	9
chemokine	8
gpcrs	8
hbond	8
helix8	8
imaging	8
bimane	7
cancer	7
channel	7
ecl2	7
gly	7
icl3	7
ionic	7
lmc_101	7
plasticity	7
protonation	7
tm3	7
w648	7
cation-pi	6
ccr5	6
conformational_changes	6
cys_scanning	6
d250	6
internalization	6
npxxy	6
opioid	6
thyrotropin	6
tm2	6
xray	6
amine	5
binding_kinetics	5
dimerization	5
dry	5
expression	5
lock	5
polymorphism	5
spectroscopy	5
thr	5
trp	5
angiotensin	4
antagonist	4
biased_agonism	4
cam	4
cholesterol	4
disorder	4
hormone	4
n749	4
nterm	4
pathway	4
tm7	4
water	4
cxcr1	3
grk	3
histamine	3
n745	3
oligomerization	3
spin_labeling	3
toac	3
webserver	3
5ht1a	2
chimera	2
crosslinking	2
em	2
leukotriene	2
lhr	2
networks	2
pathways	2
phylogeny	2
s542	2
solvation	2
tm1	2
tmhs	2
txp	2
b1ar	1
binding_site	1
class_c	1
efficacy	1
gaba	1
induced_fit	1
inverse_agonist	1
kinase	1
kinks	1
metai	1
oligomers	1
peptide	1
priviledged_structures	1
protein_docking	1
selectivity	1
sequence_alignment	1
tm4	1
transducin	1
vasopressin	1

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