dimka's library 725 articles Export

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	Ion Conduction through MscS as Determined by Electrophysiology and Simulation. [My Copy] Biophys J, Vol. 92, No. 3. (17 February 2007), pp. 886-902. by Marcos Sotomayor, Valeria Vasquez, Eduardo Perozo, Klaus Schulten posted to channel lipid membrane mscs simulation by dimka on 2006-11-28 20:25:33 as
	Lipid bilayer pressure profiles and mechanosensitive channel gating. [My Copy] Biophys J, Vol. 86, No. 6. (June 2004), pp. 3496-3509. by J. Gullingsrud, K. Schulten posted to channel gating lipid-area mechanosensitive mscl order-parameter by dimka on 2005-11-16 20:17:01 as along with 2 people sunnytov viktor21614
	Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation. [My Copy] Science, Vol. 314, No. 5801. (10 November 2006), pp. 1004-1007. by F. I. Valiyaveetil, M. Leonetti, T. W. Muir, R. Mackinnon posted to channel kcsa kir open selectivity by dimka on 2006-11-16 16:05:19 as
	A novel KCNJ11 mutation associated with congenital hyperinsulinism reduces the intrinsic open probability of beta-cell ATP-sensitive potassium channels. [My Copy] J Biol Chem, Vol. 281, No. 5. (3 February 2006), pp. 3006-3012. by Y. W. Lin, C. MacMullen, A. Ganguly, C. A. Stanley, S. L. Shyng posted to atp katp kir kir62 mutation pip2 by dimka on 2006-05-11 23:02:59 as
	Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. [My Copy] Methods Enzymol, Vol. 127 (1986), pp. 21-47. by M. Mezei, D. L. Beveridge posted to mc mmc proximity-analysis qcdf rdf by dimka on 2006-04-20 17:08:47 as
	Detailed microscopic study of the full zipA:FtsZ interface. [My Copy] Proteins (14 March 2006) by I S S. Moreira, P A A. Fernandes, M J J. Ramos posted to ala-scanning irina by dimka on 2006-03-23 03:44:51 as along with 1 person IrinaMoreira
	Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 994-999. by R. A. Estabrook, J. Luo, M. M. Purdy, et al.V. Sharma, P. Weakliem, T. C. Bruice, N. O. Reich posted to analysis coevolutionary covariance sca statistical by dimka on 2006-03-21 04:59:51 as along with 4 people and 2 groups ana barry pansapiens gbart structural_bioinformatics Bioinformatics
	Hydrogen bonding dynamics between adjacent blades in G protein beta subunit regulate GIRK channel activation. [My Copy] Biophys J (20 January 2006) by Tooraj Mirshahi, Diomedes E E. Logothetis, Avia Rosenhouse-Dantsker posted to g-protein girk by dimka on 2006-03-20 17:39:50 as
	Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model. [My Copy] J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 1. (12 January 2006), pp. 548-556. by S. Tanizaki, M. Feig posted to gb implicit md membrane protein water by dimka on 2006-03-06 16:15:20 as along with 2 people and 1 group onufriev xdeupi LabCompMed
	Model of an asymmetric DPPC/DPPS membrane: effect of asymmetry on the lipid properties. A molecular dynamics simulation study. [My Copy] J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 5. (9 February 2006), pp. 2358-2363. by J. J. López Cascales, T. F. Otero, B. D. Smith, C. González, M. Márquez posted to dppc dpps lipid membrane by dimka on 2006-03-06 16:10:53 as
	Multiple Alignment of protein structures and sequences for VMD [My Copy] Bioinformatics, Vol. 22, No. 4. (15 February 2006), pp. 504-506. by John Eargle, Dan Wright, Zaida Luthey-Schulten posted to alignment multiple protein structure by dimka on 2006-02-18 00:24:50 as along with 2 people and 2 groups jeargle marcius BioinfoCIPF SGU-CIPF
	GROMACS: fast, flexible, and free. [My Copy] J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1701-1718. by D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, H. J. Berendsen posted to dynamics gromacs md molecular simulations by dimka on 2005-12-15 21:09:26 as along with 18 people and 2 groups r2s2 janneb dsmueller oteri choonpeng sebk jwm ttjoseph bilab rabio Dinler tji softsimu ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	One channel: open and closed. [My Copy] Structure (Camb), Vol. 13, No. 10. (October 2005), pp. 1398-1400. by J. L. Robertson, B. Roux posted to close conformation cryomicroscopy electron kirbac31 open by dimka on 2005-10-23 23:03:55 as
	Ligand binding affinities from MD simulations. [My Copy] Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 358-365. by J. Aqvist, V. B. Luzhkov, B. O. Brandsdal posted to lie linear-energy-interaction md by dimka on 2005-09-30 22:09:29 as along with 4 people and 2 groups flbarroso barry baaden superpyrin structural_bioinformatics Bioinformatics
	The linear interaction energy method for predicting ligand binding free energies. [My Copy] Comb Chem High Throughput Screen, Vol. 4, No. 8. (December 2001), pp. 613-626. by J. Aqvist, J. Marelius posted to lie linear-energy-interaction theory by dimka on 2005-09-30 22:07:02 as along with 2 people flbarroso baaden
	Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. [My Copy] Biophys J, Vol. 84, No. 6. (June 2003), pp. 3636-3645. by M. Patra, M. Karttunen, M. T. Hyvönen, E. Falck, P. Lindqvist, I. Vattulainen posted to dppc dynamics lipid-area membrane molecular by dimka on 2005-09-20 22:26:26 as along with 2 people easybakemuffin softsimu
	Mechanism of rectification in inward-rectifier K+ channels. [My Copy] Annu Rev Physiol, Vol. 66 (2004), pp. 103-129. by Z. Lu posted to channel mechanism rectification review by dimka on 2005-09-19 18:30:42 as along with 1 person batallah
	Membrane protein structure quality in molecular dynamics simulation. [My Copy] J Mol Graph Model (12 August 2005) by Richard J J. Law, Charlotte Capener, Marc Baaden, et al.Peter J J. Bond, Jeff Campbell, George Patargias, Yalini Arinaminpathy, Mark S P S. Sansom posted to membrane protein review simulations by dimka on 2005-08-31 17:46:10 as along with 1 person baaden
	A phosphorylation-dependent export structure in ROMK (KIR 1.1) channel overides an ER- localization signal. [My Copy] J Biol Chem (23 August 2005) by Dana Yoo, Liang Fang, Amanda Mason, Bo-Young Y. Kim, Paul A A. Welling posted to kir11 romk by dimka on 2005-08-27 08:44:19 as along with 1 person jenni_p
	Multiple PIP2 binding sites in Kir2.1 inwardly rectifying potassium channels [My Copy] FEBS letters, Vol. 490, No. 1-2. (9 February 2001), pp. 49-53. by M. Soom, R. Schonherr, Y. Kubo, C. Kirsch, R. Klinger, S. H. Heinemann posted to channel dose-response glutathione liposomes mutation relationship site-directed structure tertiary transcription transferase by dimka on 2005-06-06 17:48:04 as
	Merging functional studies with structures of inward-rectifier K(+) channels [My Copy] Nature reviews. Neuroscience, Vol. 4, No. 12. (2003), pp. 957-967. by D. Bichet, F. A. Haass, L. Y. Jan posted to channel cytoplasm gating human inwardly ion molecular permeability potassium rectifying relationship structure structure-activity by dimka on 2005-06-06 17:47:38 as
	MD simulation of asymmetric phospholipid bilayers with ions and cholesterols [My Copy] Chem-Bio Informatics Journal, Vol. 4, No. 1. (2004), pp. 15-26. by Kenichi Mori, Masayuki Hata, Saburo Neya, Tyuji Hoshino posted to asymmetry bilayer chlesterol lipid md popc pope pops by dimka on 2006-12-10 23:36:30 as
	A novel fingerprint for the characterization of protein folds. [My Copy] Protein Eng, Vol. 16, No. 10. (October 2003), pp. 713-715. by M. Mezei posted to classification domain fingerprint by dimka on 2006-06-15 19:18:11 as
	Graph Clustering and Minimum Cut Trees [My Copy] Internet Math, Vol. 1, No. 4. (2003), pp. 385-408. by Gary W. Flake, Robert E. Tarjan, Kostas Tsioutsiouliklis posted to culstering graph tree by dimka on 2006-06-13 19:54:26 as
	Molecular Dynamics study of MscL interactions with a curved lipid bilayer. [My Copy] Biophys J (2 June 2006) by Grischa R R. Meyer, Justin Gullingsrud, Klaus Schulten, Boris Martinac posted to lipid md mechanosensitive membrane mscl simulation by dimka on 2006-06-09 18:38:04 as along with 1 person choonpeng
	Molecular dynamics simulations of unsaturated lipid bilayers: effects of varying the numbers of double bonds. [My Copy] Eur Biophys J, Vol. 34, No. 4. (June 2005), pp. 294-305. by M. T. Hyvönen, P. T. Kovanen posted to double-bond lipid md unsaturated by dimka on 2006-04-07 22:10:49 as along with 2 people priyaps softsimu
	Interaction between K(+) channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation. [My Copy] Eur Biophys J, Vol. 35, No. 5. (2 May 2006), pp. 373-381. by Manami Nishizawa, Kazuhisa Nishizawa posted to kv lipid-protein md simulation structural-modelling by dimka on 2006-02-07 18:23:58 as
	Energetics of ion conduction through the K+ channel. [My Copy] Nature, Vol. 414, No. 6859. (1 November 2001), pp. 73-77. by S. Bernèche, B. Roux posted to conductivity ion kcsa kir permeation by dimka on 2005-12-26 07:49:28 as along with 2 people and 1 group Diego_Prada brocktice TulaneCEP
	Molecular dynamics simulation of a phosphatidylglycerol membrane. [My Copy] FEBS Lett (6 December 2005) by Donald E E. Elmore posted to bilayer lipid popc popg properties simulations by dimka on 2005-12-25 22:17:34 as along with 3 people and 4 groups piscinero xdeupi softsimu Fluid-Mechanics-and-Thermal-Science-Research Computational_Systems_Biology XMLDataManagement LabCompMed
	A New Technique for Finding Needles in Haystacks: A Geometric Approach to Distinguishing Between a New Source and Random Fluctuations [My Copy] ArXiv Physics e-prints (May 2005) by R. S. Pilla, C. Loader, C. Taylor posted to montecarlo noise signal significance statistice by dimka on 2005-12-07 21:09:40 as
	Role of Aromatic Localisation in the Gating Process of a Potassium Channel. [My Copy] Biophys J (16 September 2005) by Carmen Domene, Satyavani Vemparala, Michael L L. Klein, Catherine Venien-Brian, Declan A A. Doyle posted to kirbac11 by dimka on 2005-09-26 19:20:21 as
	PIP2 signaling in lipid domains: a critical re-evaluation [My Copy] The EMBO Journal, Vol. aop, No. current. (21 April 2005) by Jacco v. van Rheenen, Eskeatnaf M. Achame, Hans Janssen, Jero Calafat, Kees Jalink posted to lipid pip2 by dimka on 2005-09-23 20:57:44 as
	PIP2 hydrolysis underlies agonist-induced inhibition and regulates voltage gating of two-pore domain K+ channels [My Copy] The Journal of Physiology, Vol. 564, No. 1. (April 2005), pp. 117-129. by M. B. Lopes, Rohacs Tibor, Czirjak Gabor, Balla Tamas, Enyedi Peter, E. Logothetis posted to gating hydrolysis k-channel pip2 two-pore by dimka on 2005-09-19 22:16:07 as
	Modeling ion channel regulation [My Copy] Current Opinion in Chemical Biology, Vol. 7, No. 6. (December 2003), pp. 710-714. by G. A. Woolley, T. Lougheed posted to gating ligand-gated mechanosensitive models proton review voltage-gated by dimka on 2005-09-01 16:11:51 as
	Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. [My Copy] Science, Vol. 309, No. 5736. (5 August 2005), pp. 897-903. by S. B. Long, E. B. Campbell, R. Mackinnon posted to channel kir kv12 open structure by dimka on 2005-08-30 16:41:09 as along with 3 people starz1010101 baniel davidcsterratt
	Differential distribution of individual subunits of strongly inwardly rectifying potassium channels (Kir2 family) in rat brain. [My Copy] Brain Res Mol Brain Res (2 June 2005) by Harald Prüss, Christian Derst, Reinhard Lommel, Rüdiger W W. Veh posted to channel irk kir2 rats subunit by dimka on 2005-08-27 08:46:37 as
	General anosmia caused by a targeted disruption of the mouse olfactory cyclic nucleotide-gated cation channel. [My Copy] Neuron, Vol. 17, No. 4. (October 1996), pp. 681-693. by L. J. Brunet, G. H. Gold, J. Ngai posted to olfactory ip3 camp by dimka on 2009-11-02 02:56:47 as
	A cyclic nucleotide-gated conductance in olfactory receptor cilia. [My Copy] Nature, Vol. 325, No. 6103. (4 1987), pp. 442-444. by T. Nakamura, G. H. Gold posted to olfactory cgmp camp by dimka on 2009-11-02 02:55:02 as along with 1 person and 1 group dark_innocent neurolit
	The Cys-loop superfamily of ligand-gated ion channels: the impact of receptor structure on function. [My Copy] Biochemical Society transactions, Vol. 32, No. Pt3. (June 2004), pp. 529-534. by C. N. Connolly, K. A. Wafford posted to glycine gating by dimka on 2009-11-02 02:47:34 as
	Cys-loop receptors: new twists and turns. [My Copy] Trends in neurosciences, Vol. 27, No. 6. (June 2004), pp. 329-336. by Henry A. Lester, Mohammed I. Dibas, David S. Dahan, John F. Leite, Dennis A. Dougherty posted to gating ach-receptor-channel by dimka on 2009-11-02 02:43:34 as
	The MARTINI Coarse-Grained Force Field: Extension to Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 5. (1 May 2008), pp. 819-834. by Luca Monticelli, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, Siewert-Jan Marrink posted to lipids coarse-grain cg bilayer by dimka on 2009-10-29 23:16:44 as along with 13 people and 3 groups arnaucordomi oteri sunrise flbarroso A_Coletta_Thesis krapnik Marine middledomain sobolevnrm Ema aqeel DanielParton softsimu Structural Biology Group TorVergata Molecular dynamics in MSU baker-group
	Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids [My Copy] Journal of the American Chemical Society, Vol. 118, No. 45. (1 January 1996), pp. 11225-11236. by William L. Jorgensen, David S. Maxwell, Julian Tirado-Rives posted to opls force-field by dimka on 2009-10-29 22:31:50 as along with 9 people snichols15 flbarroso tovrstra dfgreen sunnytov BragilMassoud loison softsimu Diego_Prada
	Interatomic potentials and solvation parameters from protein engineering data for buried residues [My Copy] Protein Science, Vol. 11, No. 8. (2002), pp. 1984-2000. by Andrei L. Lomize, Mikhail Y. Reibarkh, Irina D. Pogozheva posted to vdw sulfur potential by dimka on 2009-10-29 20:55:18 as
	A comparison of ligand based virtual screening methods and application to corticotropin releasing factor 1 receptor. [My Copy] Journal of molecular graphics & modelling, Vol. 27, No. 8. (June 2009), pp. 860-870. by Gary Tresadern, Daniele Bemporad, Trevor Howe posted to smallmol screening by dimka on 2009-10-20 17:24:00 as
	Elucidating Molecular Overlays from Pairwise Alignments Using a Genetic Algorithm [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 7. (27 July 2009), pp. 1847-1855. by Gareth Jones, Yinghong Gao, Carleton R. Sage posted to smallmol conformation bioactive by dimka on 2009-10-20 16:41:40 as along with 2 people reyez ima
	Receptor-regulated ion channels. [My Copy] Current opinion in cell biology, Vol. 9, No. 2. (April 1997), pp. 155-160. by L. Y. Jan, Y. N. Jan posted to review kir gating by dimka on 2009-10-19 06:37:42 as
	Acetylcholine receptor channel imaged in the open state. [My Copy] Nature, Vol. 373, No. 6509. (5 January 1995), pp. 37-43. by N. Unwin posted to ach-receptor-channel ach by dimka on 2009-10-19 06:25:22 as
	Molecular insights into ion channel function (Review). [My Copy] Molecular membrane biology, Vol. 21, No. 4. (g 2004), pp. 221-225. by Declan A. Doyle posted to structure-activity review kir by dimka on 2009-10-19 06:22:42 as
	Stabilization of the activity of ATP-sensitive potassium channels by ion pairs formed between adjacent Kir6.2 subunits. [My Copy] The Journal of general physiology, Vol. 122, No. 2. (August 2003), pp. 225-237. by Yu-Wen W. Lin, Taiping Jia, Anne M. Weinsoft, Show-Ling L. Shyng posted to kir62 katp by dimka on 2009-10-19 06:19:29 as
	Mapping of the physical interaction between the intracellular domains of an inwardly rectifying potassium channel, Kir6.2. [My Copy] The Journal of biological chemistry, Vol. 274, No. 47. (19 November 1999), pp. 33393-33397. by S. J. Tucker, F. M. Ashcroft posted to kir62 katp domain by dimka on 2009-10-19 06:17:46 as

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pip2	100
md	99
channel	85
structure	84
lipid	81
membrane	72
kir	61
protein	61
mmult-ref	59
gating	47
simulation	47
molecular	44
phosphatidylinositol	38
potassium	38
simulations	38
review	37
ph	34
ph-sensor	33
sequence	33
romk	29
ion	25
katp	24
alignment	22
bilayer	22
conformation	21
dppc	21
kir62	21
classification	20
kcsa	20
models	20
irk1	19
kir21	17
binding	15
electrostatics	15
inositol	15
mutation	15
peptide	14
amp	13
domain	12
inwardly	12
kir11	12
mutagenesis	12
adenosine	11
analysis	11
cholesterol	11
crystallography	11
electrophysiology	11
gtp-binding	11
tertiary	11
triphosphate	11
dmpc	10
girk	10
g-protein	10
kinetics	10
multiple	10
charmm	9
conductivity	9
free-energy	9
homology	9
humans	9
inhibitor	9
model	9
nmr	9
patch-clamp	9
pore	9
smallmol	9
structure-activity	9
thermodynamics	9
automatic	8
coarse-grain	8
fluorescence	8
girk1	8
headgroup	8
kir31	8
kir41	8
kirbac11	8
kv12	8
ligand	8
open-closed	8
phospholipase	8
phosphorylation	8
proteins	8
atp	7
calcium	7
force-field	7
gromacs	7
methods	7
pca	7
phosphate	7
phosphoinositides	7
protein-lipid	7
rats	7
recombinant	7
relationship	7
scop	7
site-directed	7
sites	7
transduction	7
ach	6
activation	6
chimera	6
deltag	6
disease	6
dna	6
dynamics	6
folding	6
heart	6
interaction	6
kir23	6
kv	6
laevis	6
microscopy	6
open	6
permeation	6
phosphatidylcholine	6
popc	6
rectify	6
secondary	6
signal	6
sodium	6
software	6
specificity	6
voltage-gated	6
cations	5
cell	5
diffusion	5
enzyme	5
guanosine	5
heterotrimeric	5
identification	5
ip3	5
kir34	5
lipid-area	5
md-analysis	5
mechanosensitive	5
membrane-protein	5
mscl	5
muscarinic	5
myocardium	5
namd	5
orientation	5
partition	5
polyamines	5
rectifying	5
selectivity	5
techniques	5
tool	5
voltage	5
1-phosphatidylinositol	4
algorithm	4
bacterial	4
blocker	4
blood	4
chemistry	4
concentration	4
crystal	4
cytoplasm	4
database	4
derivatives	4
desease	4
desmond	4
dopc	4
electrostatic	4
equilibration	4
hydrogen-ion	4
hydrolysis	4
implicit	4
inhibition	4
inositiol	4
irk3	4
kir51	4
kirbac31	4
lipid-protein	4
modeling	4
modeller	4
montecarlo	4
pdb	4
phosphoprotein	4
pip3	4
pressure	4
receptor	4
rectification	4
single-channel	4
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trajectory	4
transport	4
3-kinase	3
ab-initio	3
ach-receptor-channel	3
acyl-coa	3
assembly	3
bartter	3
biological	3
biophysics	3
book	3
brownian	3
charge	3
charmm27	3
chemical	3
comparative	3
compare	3
competitive	3
computation	3
cultured	3
cysteine	3
cytoplasmic	3
cytoskeleton	3
cytosol	3
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diffraction	3
dimyristoyl	3
distribution	3
docking	3
drug-design	3
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electric	3
experimental	3
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fep	3
force-fields	3
gb	3
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girk4	3
glycine	3
gromos	3
growth	3
helix	3
implicit-membrane	3
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k-channel	3
kir2	3
kir3	3
kvap	3
lc-coa	3
lipid-order-parameter	3
macromolecular	3
magnesium	3
mcd	3
mechanism	3
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andersen	2
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bonding	2
camp	2
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cho	2
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porin	2
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transcription	2
tree	2
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water	2
110-decanediamine	1
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2-naphthylamine	1
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4-aminopyridine	1
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chloride	1
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cloning	1
close	1
coated	1
coenzyme	1
coevolutionary	1
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complex	1
compound	1
computer-assisted	1
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contact	1
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cryem	1
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csp	1
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culstering	1
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da10	1
da12	1
dag	1
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density	1
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dppe	1
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em	1
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ethyl	1
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glycosylphosphatidylinositols	1
gpcr	1
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hela	1
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ige	1
iglur	1
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immunology	1
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npt	1
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oleic	1
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ompf	1
ompla	1
oocytes	1
opls	1
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pc	1
pdpc	1
percent	1
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pho-his	1
phosphatase	1
phosphates	1
phosphatidylethanolamine	1
phospho	1
phosphoric	1
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pi34p2	1
pi3k	1
pi-3-kinase	1
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pis	1
pka	1
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plc	1
pme	1
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potasium	1
pregs	1
pro	1
probability	1
proline	1
protein_structure	1
protein-structure	1
protein-tyrosine	1
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ptx	1
pxoom	1
pyrophosphorylation	1
qcdf	1
qm	1
qt	1
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ras	1
rattle	1
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rev1	1
rhodopsin	1
ribonuclease	1
rip	1
rosetta	1
russian	1
s143f	1
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sca	1
scattering	1
science	1
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screening	1
sdf	1
second	1
secretory	1
sensor	1
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sequence-structure	1
server	1
setup	1
shake	1
shape	1
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silver	1
simulaiton	1
simulstions	1
small	1
sodium_channel	1
sodium-gating	1
solvents	1
spermine	1
sse	1
stability	1
states	1
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staurosporine	1
stimulation	1
structural-modelling	1
structures	1
strucure	1
substances	1
subunit	1
sulf	1
sulfonyurea	1
sulfur	1
superfamily	1
sur1	1
sur2	1
synaptic	1
systems	1
tendem	1
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thickness	1
thionucleotide	1
transferase	1
transformation	1
transmembrane	1
trehalose	1
trp8	1
trp-channel	1
trpm4	1
tubules	1
two-pore	1
typology	1
v302m	1
vector	1
venom	1
viewer	1
viral	1
voltage-sensor	1
volume	1
water-protein	1

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