dimka's md [100 articles] Export

Recent papers added to dimka's library classified by the tag md. You can also see everyone's md.

	Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR. [My Copy] Journal of biomolecular NMR, Vol. 32, No. 2. (June 2005), pp. 151-162. by Hao Hu, Jan Hermans, Andrew L. Lee posted to timescale rotamer md by dimka on 2009-11-16 19:00:27 as along with 1 person lna
	Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: The myoglobin case [My Copy] Journal of Molecular Graphics and Modelling, Vol. 27, No. 8. (June 2009), pp. 889-899. by Elena Papaleo, Paolo Mereghetti, Piercarlo Fantucci, Rita Grandori, Luca De Gioia posted to pca md analyais by dimka on 2009-10-14 23:51:37 as along with 1 person anuragsethi
	Molecular Dynamics Simulation Study of Correlated Motions in Phospholipid Bilayer Membranes [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13229-13234. by Matthew Roark, Scott E. Feller posted to membrane md lipid diffusion_coefficients bilayer by dimka on 2009-09-17 19:11:29 as along with 2 people sobolevnrm agrossfield
	Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations [My Copy] Journal of Computational Physics, Vol. 52, No. 1. (October 1983), pp. 24-34. by H. Andersen posted to rattle methods md by dimka on 2009-08-20 07:12:56 as along with 1 person horaciotm
	Constant pressure molecular dynamics simulation: The Langevin piston method [My Copy] The Journal of Chemical Physics, Vol. 103, No. 11. (1995), pp. 4613-4621. by Scott E. Feller, Yuhong Zhang, Richard W. Pastor, Bernard R. Brooks posted to algorithm md nose-hoover pressure by dimka on 2009-08-05 07:06:49 as along with 2 people rpetrenko easybakemuffin
	Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension [My Copy] Biophysical Journal, Vol. 92, No. 12. (15 June 2007), pp. 4157-4167. by J. Sonne, M. Jensen, F. Hansen, L. Hemmingsen, G. Peters posted to charmm lipids md parameterization by dimka on 2009-07-27 20:29:25 as along with 1 person arnaucordomi
	All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data [My Copy] Journal of Computational Chemistry, Vol. 21, No. 2. (2000), pp. 86-104. by Nicolas Foloppe, Alexander D. Mackerell, Jr posted to charmm charmm27 force-field lipid md by dimka on 2009-07-27 20:26:34 as along with 3 people rpetrenko mkrishna easybakemuffin
	Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000343. by Bosco K. Ho, David A. Agard posted to analysis md rip by dimka on 2009-07-15 17:03:07 as along with 5 people and 3 groups skywalkerus02 operon sobolevnrm barry bourby baker-group structural_bioinformatics McCammon
	Molecular Dynamics Simulations of PIP2 and PIP3 in Lipid Bilayers: Determination of Ring Orientation, and the Effects of Surface Roughness on a Poisson-Boltzmann Description [My Copy] Biophysical Journal, Vol. 97, No. 1. (08 July 2009), pp. 155-163. by Zheng Li, Richard M. Venable, Laura A. Rogers, Diana Murray, Richard W. Pastor posted to bilayer lipid md pip2 pip3 simulation by dimka on 2009-07-08 21:33:21 as
	Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation. [My Copy] Journal of the American Chemical Society, Vol. 131, No. 13. (8 April 2009), pp. 4854-4865. by Brett N. Olsen, Paul H. Schlesinger, Nathan A. Baker posted to cholesterol lipid md popc simulation by dimka on 2009-06-30 20:49:00 as along with 1 person and 1 group sobolevnrm baker-group
	Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 27. (9 July 2009), pp. 9183-9196. by Joseph E. Davis, Sandeep Patel posted to c27r dmpc dppc md simulation by dimka on 2009-06-19 19:28:42 as along with 1 person agrossfield
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. Brooks, C. L. Brooks, A. D. Mackerell, et al.L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus posted to charmm md program by dimka on 2009-05-16 20:16:32 as along with 8 people and 1 group rodrigofaccioli mmuecke medic0747 flbarroso jrperillaj xavierprat saravan sobolevnrm baker-group
	Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 3. (10 March 2009), pp. 615-626. by Andreas Kukol posted to bilayer lipid md order-parameter simulation by dimka on 2009-04-06 22:31:56 as along with 3 people and 1 group arnaucordomi Marine middledomain Molecular dynamics in MSU
	Molecular dynamics study of unbinding of the avidin-biotin complex. [My Copy] Biophysical journal, Vol. 72, No. 4. (April 1997), pp. 1568-1581. by S. Izrailev, S. Stepaniants, M. Balsera, Y. Oono, K. Schulten posted to lipid md pull smd by dimka on 2008-12-26 06:21:54 as
	Extraction of Lipids from Phospholipid Membranes by Steered Molecular Dynamics [My Copy] Journal of Molecular Modeling, Vol. 3, No. 12. (1 December 1997), pp. 473-475. by Sergey Stepaniants, Sergei Izrailev, Klaus Schulten posted to lipid md namd pull smd by dimka on 2008-12-26 05:23:45 as along with 1 person sunnytov
	Molecular Dynamic Simulation of the Kv1.2 Voltage-Gated Potassium Channel in Open and Closed State Conformations [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 51. (25 December 2008), pp. 16966-16974. by Ming Han, John Z. Zhang posted to kv12 md open-closed by dimka on 2008-12-21 23:54:02 as
	Molecular Coordinates of Pre-Equilibrated Lipid Systems [My Copy] by J. B. Klauda posted to equilibration lipid md membane by dimka on 2008-11-30 23:40:22 as
	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 lipid md membrane simulation by dimka on 2008-11-11 21:48:17 as along with 3 people and 1 group xdeupi easybakemuffin viktor21614 LabCompMed
	The molecular face of lipid rafts in model membranes [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 45. (11 November 2008), pp. 17367-17372. by H. Jelger Risselada, Siewert J. Marrink posted to lipid md mixture simulations by dimka on 2008-11-07 20:27:12 as along with 8 people and 2 groups richardfranzese ARobson wsjames reister paulschlesinger chiufanlee barry kshundyak Oxford Virology McCammon
	Hydration forces between phospholipid bilayers [My Copy] Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, Vol. 988, No. 3. (06 December 1989), pp. 351-376. by R. Rand posted to equilibration lipid md membrane review simulation by dimka on 2008-10-29 00:10:07 as along with 2 people scampos softsimu
	Dynamic control of slow water transport by aquaporin 0: Implications for hydration and junction stability in the eye lens [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (23 September 2008), pp. 14430-14435. by Morten Jensen, Ron O. Dror, Huafeng Xu, et al.David W. Borhani, Isaiah T. Arkin, Michael P. Eastwood, David E. Shaw posted to aquaporin desmond md by dimka on 2008-10-16 18:43:08 as along with 2 people qshao agrossfield
	Determination of component volumes of lipid bilayers from simulations. [My Copy] Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2237-2242. by H. I. Petrache, S. E. Feller, J. F. Nagle posted to dppc lipid md methods simulations volume by dimka on 2008-09-25 21:02:11 as
	A sodium-mediated structural switch that controls the sensitivity of Kir channels to PtdIns(4,5)P(2). [My Copy] Nature chemical biology (14 September 2008) by Avia Rosenhouse-Dantsker, Jin L L. Sui, Qi Zhao, et al.Radda Rusinova, Aldo A A. Rodríguez-Menchaca, Zhe Zhang, Diomedes E E. Logothetis posted to kir md pip2 sodium by dimka on 2008-09-17 17:49:36 as
	Molecular dynamics simulation of hydrated phospholipid bilayers. [My Copy] Indian journal of biochemistry & biophysics, Vol. 33, No. 6. (December 1996), pp. 431-447. by V. Kothekar posted to dmpc lipid md membrane simulation by dimka on 2008-08-20 19:33:30 as
	Cholesterol Packing around Lipids with Saturated and Unsaturated Chains: A Simulation Study [My Copy] Langmuir (3 June 2008) by Sagar A. Pandit, See-Wing Chiu, Eric Jakobsson, Ananth Grama, H. L. Scott posted to cholesterol dopc md simulation by dimka on 2008-08-18 22:53:18 as along with 2 people and 1 group paulschlesinger sobolevnrm baker-group
	Effective Mast Cell Degranulating Peptide Inhibitors of the IgE/FcepsilonRI Receptor Interaction. [My Copy] Chemical biology & drug design (3 July 2008) by Angeliki Buku, Inna Keselman, Dmitry Lupyan, Mihaly Mezei, Joseph A A. Price posted to ige ige-receptor mcd md peptide simulation by dimka on 2008-07-29 21:44:13 as along with 1 person yanz
	Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters [My Copy] Supercomputing, 2006. SC '06. Proceedings of the ACM/IEEE SC 2006 Conference In Supercomputing, 2006. SC '06. Proceedings of the ACM/IEEE SC 2006 Conference (2006), pp. 43-43. by K. J. Bowers, E. Chow, Huafeng Xu, et al.R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Yibing Shan, D. E. Shaw posted to algorithm desmond engine md by dimka on 2008-07-24 19:09:14 as
	Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations [My Copy] Biophys. J., Vol. 95, No. 4. (15 August 2008), pp. 1866-1876. by Philip D. Blood, Richard D. Swenson, Gregory A. Voth posted to md pip2 by dimka on 2008-07-24 18:37:03 as
	Mechanism of Na+/H+ Antiporting [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 799-803. by Isaiah T. Arkin, Huafeng Xu, Morten O. Jensen, et al.Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman-Tene, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Yibing Shan, David E. Shaw posted to desmond md membrane simulation by dimka on 2008-07-08 21:34:50 as along with 6 people and 1 group Diego_Prada allmensch sobolevnrm Jporci MMehrotra LamBras baker-group
	Conformational Changes and Gating at the Selectivity Filter of Potassium Channels [My Copy] J. Am. Chem. Soc. (28 June 2008) by Carmen Domene, Michael L. Klein, Davide Branduardi, Francesco L. Gervasio, Michele Parrinello posted to kirbac lipid md selectivity simulation by dimka on 2008-07-01 00:10:09 as
	Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions [My Copy] J. Phys. Chem. B, Vol. 108, No. 14. (8 April 2004), pp. 4485-4494. by M. Patra, M. Karttunen, M. T. Hyvonen, E. Falck, I. Vattulainen posted to dppc gromacs md simulations by dimka on 2008-06-27 04:38:49 as along with 1 person softsimu
	Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers [My Copy] European Biophysics Journal, Vol. 37, No. 2. (11 February 2008), pp. 131-141. by Katherine Cox, Peter Bond, Alessandro Grottesi, Marc Baaden, Mark Sansom posted to compare md membrane protein simulation by dimka on 2008-06-25 16:48:52 as
	Interactions of the Pleckstrin Homology Domain with Phosphatidylinositol Phosphate and Membranes: Characterization via Molecular Dynamics Simulations [My Copy] Biochemistry, Vol. 47, No. 14. (15 March 2008), pp. 4211-4220. by Emi Psachoulia, Mark S. Sansom posted to inositiol md phosphoinositides protein-ligand protein-lipid protein-membrane simulations by dimka on 2008-05-28 22:02:54 as along with 2 people choonpeng paulschlesinger
	Essential dynamics of proteins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 17, No. 4. (December 1993), pp. 412-425. by Andrea Amadei, Antonius B. M. Linssen, Herman J. C. Berendsen posted to dynamics md md-analysis pca simulations by dimka on 2008-05-14 01:42:48 as along with 10 people and 1 group kazemi Diego_Prada baaden aqeel yongzhao ttjoseph ffranca allmensch carlescorbi nigham TSRI_MGL
	Simulaid [My Copy] http://atlas.physbio.mssm.edu/~mezei/simulaid/ by Mihaly Mezei posted to analysis md md-analysis simulaid by dimka on 2008-05-14 01:35:17 as
	Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating. [My Copy] Biophysical journal, Vol. 88, No. 5. (May 2005), pp. 3310-3320. by S. Haider, A. Grottesi, B. A. Hall, F. M. Ashcroft, M. S. Sansom posted to katp kir md simulations by dimka on 2008-05-14 00:48:45 as along with 1 person mengcite
	Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study [My Copy] Biophys. J., Vol. 88, No. 6. (1 June 2005), pp. 3822-3828. by Steve O. Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B. Moore, Michael L. Klein posted to lipid md nanotube perturbation simulation by dimka on 2008-05-13 21:14:16 as along with 2 people Marine loison
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, Alex H. de Vries posted to coarse-grain force-field md simulations by dimka on 2008-05-13 21:10:45 as along with 7 people and 2 groups anuragsethi sunrise A_Coletta_Thesis Marine choonpeng softsimu sunnytov Structural Biology Group TorVergata Molecular dynamics in MSU
	Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1113-1130. by Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang, Kim A. Sharp posted to charged implicit-water md simulations by dimka on 2008-05-13 21:00:30 as along with 5 people and 1 group ras Elena_Zubova sobolevnrm RamuAnandakrishnan onufriev baker-group
	Focus on Kir6.2: a key component of the ATP-sensitive potassium channel. [My Copy] Journal of molecular and cellular cardiology, Vol. 38, No. 6. (June 2005), pp. 927-936. by S. Haider, J. F. Antcliff, P. Proks, M. S. Sansom, F. M. Ashcroft posted to atp katp kir62 md simulation by dimka on 2008-05-09 21:33:30 as
	Molecular dynamics simulations of potassium channels [My Copy] Central European Journal of Chemistry, Vol. 5, No. 3. (2007), pp. 635-671. by Carmen Domene posted to channels kir md review simulation by dimka on 2008-05-08 23:28:34 as
	Sodium Coordination Site Reveals a Novel Sodium-Sensitive Phenotype in Kir Channels [My Copy] In Preparation (2008) by Avia Rosenhouse-Dantsker, Jun L. Sui, Qu Zhao, Radda Rusinova, Diomedes E. Logothetis posted to kir md sodium by dimka on 2008-05-08 16:56:32 as
	Molecular dynamics simulations of membrane proteins. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 443 (2008), pp. 147-160. by P. C. Biggin, P. J. Bond posted to md membrane-protein review simulations by dimka on 2008-05-01 15:18:37 as
	The Role of Conformation in Ion Permeation in a K+ Channel [My Copy] J. Am. Chem. Soc. (23 February 2008) by C. Domene, S. Vemparala, S. Furini, K. Sharp, M. L. Klein posted to kirbac11 lipid md permeation simulation by dimka on 2008-02-25 00:44:04 as
	Hydrogen Bonding and Binding of Polybasic Residues with Negatively Charged Mixed Lipid Monolayers. [My Copy] Langmuir (23 January 2008) by Christian D. Lorenz, Jordi Faraudo, Alex Travesset posted to charmm dopc dops force-field lipid md membrane pip2 simulations by dimka on 2008-01-24 14:42:43 as along with 1 person priyaps
	Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems [My Copy] Journal of Chemical Physics*, Vol. 98, No. 12. (15 June 1993), pp. 10089-10092. by Tom Darden, Darrin York, Lee Pedersen posted to md methods pme by dimka on 2008-01-08 00:17:58 as
	Molecular Dynamics Simulations of Ternary Membrane Mixture: Phosphatidylcholine, Phosphatidic Acid, and Cholesterol. [My Copy] J Phys Chem B (5 December 2007) by Mary H. Cheng, Lu T. Liu, Alexander C. Saladino, Yan Xu, Pei Tang posted to lipid md membrane mixture simulations by dimka on 2007-12-11 00:17:42 as along with 2 people and 1 group sobolevnrm easybakemuffin baker-group
	Dynamics of the Kv1.2 Voltage-Gated K+ Channel in a Membrane Environment [My Copy] Biophys. J., Vol. 93, No. 9. (1 November 2007), pp. 3070-3082. by Vishwanath Jogini, Benoit Roux posted to kv12 md membrane potential simulations voltage by dimka on 2007-11-29 19:32:56 as along with 1 person paulschlesinger
	Dynamic Relationships among Type IIa Bacteriocins: Temperature Effects on Antimicrobial Activity and on Structure of the C-Terminal Amphipathic Alpha-Helix as a Receptor-Binding Region [My Copy] Biochemistry, Vol. 43, No. 28. (20 July 2004), pp. 9009-9020. by K. Kaur, L. C. Andrew, D. S. Wishart, J. C. Vederas posted to folding md peptide simulation by dimka on 2007-11-20 20:30:34 as
	The structure of ghrelin. [My Copy] Vitam Horm, Vol. 77 (2007), pp. 1-12. by A. Kukol posted to md peptide simulations by dimka on 2007-11-10 02:14:55 as

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md	100
pip2	100
channel	85
structure	84
lipid	81
membrane	72
kir	61
protein	61
mmult-ref	60
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
free-energy	10
girk	10
g-protein	10
kinetics	10
multiple	10
charmm	9
conductivity	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
deltag	7
force-field	7
gromacs	7
methods	7
pca	7
phosphate	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
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
phosphoinositides	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
modeling	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
distribution	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
modeller	4
montecarlo	4
pdb	4
phosphoprotein	4
pip3	4
pressure	4
receptor	4
rectification	4
single-channel	4
synthesis	4
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
data	3
diffraction	3
dimyristoyl	3
docking	3
drug-design	3
effects	3
electric	3
experimental	3
factor	3
fep	3
force-fields	3
function	3
gb	3
girk2	3
girk4	3
glycine	3
gromos	3
growth	3
helix	3
implicit-membrane	3
isoenzyme	3
k-channel	3
kir2	3
kir3	3
kvap	3
lc-coa	3
lipid-order-parameter	3
macromolecular	3
magnesium	3
mcd	3
mechanism	3
mice	3
mmpbsa	3
oocyte	3
pb	3
pcm	3
permeability	3
perturbation	3
physiology	3
pi	3
pip2-binding	3
pkc	3
popg	3
potential	3
predict	3
program	3
protein-membrane	3
pull	3
rdf	3
receptors	3
recording	3
rubidium	3
scd	3
shaker	3
smd	3
spectroscopy	3
statistics	3
syndrome	3
temperature	3
transfection	3
2d	2
5-o-3-thiotriphosphate	2
acetate	2
acetylcholine	2
ala	2
alcohol	2
allosteric	2
amino	2
andersen	2
antagonist	2
antibody	2
arachidonic	2
area	2
arginine	2
assesment	2
atria	2
autodock	2
barium	2
bd	2
beta-gamma	2
binding-energy	2
bioinformatics	2
bonding	2
camp	2
carrier	2
catalytic	2
cath	2
cells	2
cercopithecus	2
charged	2
charges	2
cho	2
clathrin	2
cma	2
co2	2
coa	2
computational	2
correlated	2
covariance	2
databases	2
definition	2
derivative	2
dielectric	2
diglycerides	2
dose-response	2
dpps	2
dynamic	2
electron	2
epidermal	2
epsin	2
esp	2
essential_dynamics	2
exchange	2
fab	2
fingerprint	2
fragment	2
fragments	2
gaussian	2
gelsolin	2
gene	2
glutathione	2
gpcr	2
graph	2
hbc	2
hinge	2
human	2
hydrophobicity	2
ied	2
ige-receptor	2
kcnq	2
kinase	2
kir6	2
kirbac	2
kv11	2
library	2
lie	2
ligands	2
linear-energy-interaction	2
lipids	2
liposome	2
liposomes	2
long	2
luminescent	2
lysine	2
m1	2
m2	2
magnetic	2
mammoth	2
mathematics	2
mc	2
memory	2
method	2
microfilament	2
mixture	2
mscs	2
muscle	2
nerve	2
nose-hoover	2
nucleotide	2
nucleus	2
olfactory	2
order-parameter	2
parameterization	2
pcf	2
phosphatidylserine	2
phosphinositides	2
phospholipid	2
phosphotransferase	2
poisson-bolzmann	2
pops	2
porin	2
potentials	2
properties	2
prostein	2
protein-ligand	2
protocol	2
proton	2
protonation	2
pseudomallei	2
quantum	2
quaternary	2
radiation	2
replica	2
resonance	2
sampling	2
score	2
sequesteration	2
sequestering	2
simulaid	2
solvation	2
spectrometry	2
statistical	2
stoichiometry	2
substitution	2
substrate	2
subunits	2
surface	2
tea	2
tetradecanoylphorbol	2
theory	2
transcription	2
tree	2
trp	2
tutorial	2
unsaturated	2
vdw	2
vesicle	2
visualization	2
vmd	2
water	2
110-decanediamine	1
1-12-dodecanediamine	1
2-naphthylamine	1
3d-to-2d	1
3-ribose	1
45-bisphosphate	1
4-aminopyridine	1
abundance	1
academy	1
achr	1
actin-binding	1
adaptor	1
afm	1
ala-scanning	1
alignments	1
alpha-hemolysin	1
alzheimers	1
amber	1
aminopyridine	1
amyloid-beta	1
analog	1
analogs	1
analyais	1
androstadiene	1
angie	1
animal	1
annotation	1
antiarrhythmic	1
anti-bacterial	1
aquaporin	1
aspartic	1
assay	1
asymmetry	1
atpase	1
atp-binding	1
b5	1
ba	1
bacteriorhodopsin	1
bayes	1
benchmark	1
beta-adrenoceptor	1
bilayers	1
binding-site	1
bioactive	1
biosynthesis	1
blocking	1
bonds	1
build	1
bundle-crossing	1
burkholderia	1
c27r	1
ca-activated	1
ca-binding	1
ca-channel	1
cadmium	1
calcium-activated	1
calculation	1
calmodulin	1
calorimetry	1
carbohydrate	1
ca-release	1
carvedilol	1
catalysis	1
cavities	1
ccdc	1
cell-membrane	1
cg	1
cgmp	1
channel-forming	1
channels	1
charmm22	1
chirality	1
chlesterol	1
chloride	1
circadian	1
circular_variance	1
clasification	1
cloning	1
close	1
coated	1
coenzyme	1
coevolutionary	1
complementary	1
complex	1
compound	1
computer-assisted	1
conduction	1
conformation-energy	1
contact	1
coupling	1
cross-talk	1
cryem	1
cryo-em	1
cryomicroscopy	1
csp	1
c-term	1
culstering	1
current-voltage	1
curvature	1
cytochrome	1
cytology	1
da10	1
da12	1
dag	1
dali	1
databank	1
defect	1
density	1
desensitization	1
deuterium	1
development	1
diabetes	1
diffusion_coefficients	1
diphosphate	1
divalent	1
dlpc	1
dope_score	1
dopg	1
dops	1
double-bond	1
dppe	1
droplet	1
dyes	1
dynanics	1
effect	1
elastic	1
elasticity	1
electron-microscope	1
electrophoresis	1
electrophy	1
electrostatic-complementarity	1
em	1
embryo	1
emf	1
endocytosis	1
endothelin	1
endothelin-1	1
energy	1
engine	1
enm	1
equation	1
er	1
ergosterol	1
escherichia	1
estrene	1
ethanol	1
ethyl	1
eukaryotic	1
evolution	1
excitation	1
expression	1
factors	1
factual	1
fast	1
fatty	1
fes	1
fitting	1
fluoremetry	1
fluorescent	1
fluorometry	1
fret	1
fssp	1
functional	1
fusion	1
generalized-born	1
genetic	1
gentamicin	1
glutamate	1
glutamic	1
glutamine	1
glycogen	1
glycoside	1
glycosylphosphatidylinositols	1
gpi	1
gramicidin	1
grasp	1
gtp-bp	1
guanylyl	1
guinea	1
hamsters	1
hela	1
heme	1
herg	1
histidine	1
history	1
h-k-exchanging	1
hole	1
homotetrameric	1
hydrogen	1
hydrogen-bond	1
hydrolase	1
hypoglycemic	1
hyrdoxyl	1
ige	1
iglur	1
ikvol	1
imidazole	1
imidodiphosphate	1
immunology	1
implicit-water	1
indole	1
insert	1
insertion	1
insertional	1
insulin-like	1
integration	1
inward	1
ionic-strength	1
ip7	1
irina	1
irk	1
ischemia	1
isoenzymes	1
isomer	1
isomerism	1
isostar	1
kidney	1
kinases	1
kir32	1
kir4	1
kir42	1
kir451	1
kir71	1
kirback	1
knockout	1
ktp	1
kv13	1
kv21	1
kv7	1
kv_modifier	1
lambda	1
leach	1
leucine	1
ligand-gated	1
light	1
ligplot	1
linoleic	1
lipd	1
lipid-water	1
magnisium-gating	1
mammals	1
marcks	1
markov	1
mc-phs	1
med	1
melanogaster	1
melitten	1
membane	1
membrane-effect	1
membrane_potential	1
messenger	1
mesylates	1
methanobacterium	1
methodology	1
micelles	1
mixing	1
mm	1
mmc	1
mmgbsa	1
mmmc	1
modulation	1
molden	1
monoclonal	1
monoester	1
monomeric	1
motifs	1
motion	1
msa	1
mthk	1
muscular	1
nanotube	1
naphthalene	1
neomycin	1
neurofibromin	1
neurons	1
neuropeptides	1
neutrons	1
nicotinic	1
nma	1
noise	1
non-bonded	1
normal	1
npt	1
nuclear	1
numerical	1
oleic	1
oligopeptide	1
ompf	1
ompla	1
oocytes	1
opls	1
optimize	1
organization	1
osmosis	1
osmotic	1
oxidation-reduction	1
oxidative	1
pairwise	1
paralyses	1
pc	1
pdpc	1
percent	1
phase	1
phenylalanine	1
phenylephrine	1
pho-his	1
phosphatase	1
phosphates	1
phosphatidylethanolamine	1
phospho	1
phosphoric	1
physical	1
pi34p2	1
pi3k	1
pi-3-kinase	1
piperazine	1
piperidine	1
pips	1
pis	1
pka	1
plants	1
plasmid	1
plc	1
pme	1
polyamine	1
polylysine	1
polymerase	1
pope	1
pore_dimensions	1
porosity	1
potasium	1
pregs	1
pro	1
probability	1
proline	1
protein_structure	1
protein-structure	1
protein-tyrosine	1
proximity-analysis	1
ptx	1
pxoom	1
pyrophosphorylation	1
qcdf	1
qm	1
qt	1
quality	1
r	1
radii	1
radioisotopes	1
ras	1
rattle	1
recognition	1
rectifier	1
reference	1
regression	1
residue-covariation	1
rev1	1
rhodopsin	1
ribonuclease	1
rip	1
rosetta	1
rotamer	1
russian	1
s143f	1
sarcolem	1
sca	1
scattering	1
science	1
scorpion	1
screening	1
sdf	1
second	1
secretory	1
sensor	1
sequence-identity	1
sequence-structure	1
server	1
setup	1
shake	1
shape	1
significance	1
silver	1
simulaiton	1
simulstions	1
small	1
sodium_channel	1
sodium-gating	1
solvents	1
spermine	1
sse	1
stability	1
states	1
statistice	1
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
template	1
tendem	1
terminology	1
tertiapin	1
thickness	1
thionucleotide	1
timescale	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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