ライフサイエンスコーパス: molecular dynamics simulation

1 ance (NMR) spectroscopy studies and all-atom molecular dynamics simulation.

2 d thermal scanning, validated by independent molecular dynamics simulation.

3 g deuterium labeling, neutron scattering and molecular dynamics simulation.

4 water spreading on hydrophobic surfaces via molecular dynamics simulation.

5 nism was probed using quantum mechanical and molecular dynamics simulations.

6 ly and compared to standard replica exchange molecular dynamics simulations.

7 les is further unraveled by explicit solvent molecular dynamics simulations.

8 whose key features can be recapitulated with molecular dynamics simulations.

9 hese bilayer heights were investigated using molecular dynamics simulations.

10 ctures and investigated their stability with molecular dynamics simulations.

11 ically by both density functional theory and molecular dynamics simulations.

12 mic allostery in a PDZ3 domain protein using molecular dynamics simulations.

13 spectroscopy, native mass spectrometry, and molecular dynamics simulations.

14 ing rigid body constraint on each residue in molecular dynamics simulations.

15 vibrational spectroscopy in combination with molecular dynamics simulations.

16 ral dynamics of Aqy1 during freezing through molecular dynamics simulations.

17 Aop-containing collagen triple helices, and molecular dynamics simulations.

18 onductance and selectivity based on all-atom molecular dynamics simulations.

19 ic glass nanowires prepared by casting using molecular dynamics simulations.

20 CRF(12-41)-bound CRF1R, further explored by molecular dynamics simulations.

21 y aspects of the hypotheses generated by the molecular dynamics simulations.

22 lding pathway, as previously postulated from molecular dynamics simulations.

23 facilitating interpretation of the data with molecular dynamics simulations.

24 arly 200 mus of residue-based coarse-grained molecular dynamics simulations.

25 only in the HRM experiments but also in the molecular dynamics simulations.

26 erties of these assemblies through atomistic molecular dynamics simulations.

27 rane depending on their surface chemistry by molecular dynamics simulations.

28 d, guided by X-ray crystallographic data and molecular dynamics simulations.

29 g technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations.

30 multiple Widom lines in binary mixtures from molecular dynamics simulations.

31 gate the sensors in vitro and in vivo and by molecular dynamics simulations.

32 broken by shear force as revealed by steered molecular dynamics simulations.

33 ly implemented in any software for atomistic molecular dynamics simulations.

34 ts can be downloaded and immediately used in molecular dynamics simulations.

35 allosteric mechanism revealed by microsecond molecular dynamics simulations.

36 nformational ensemble of BAK1 using all-atom molecular dynamics simulations.

37 one transition state, which is confirmed by molecular dynamics simulations.

38 the distortions observed in fully atomistic molecular dynamics simulations.

39 roperties of the OMs and OprH using all-atom molecular dynamics simulations.

40 lucose transporter structural dynamics using molecular-dynamics simulations.

41 and compare our findings with predictions of molecular-dynamics simulations.

42 g model employing an integrated experimental-molecular dynamics simulation (200 ns) approach.

43 talk and hinge determined based on a 3.3-mus molecular dynamics simulation account for the degree of

44 Co-crystallography and molecular dynamics simulation analyses reveal that these

45 We use a combination of molecular dynamics simulation and atomic force microscop

46 apshot approach combined with coarse-grained molecular dynamics simulation and master equation analys

47 The molecular dynamics simulation and site-directed mutagene

48 incapable of prenyl binding, is supported by molecular dynamics simulations and appears to underlie t

49 Comparison of our experimental findings with molecular dynamics simulations and density functional th

50 The method combines molecular dynamics simulations and density functional th

51 his work, we have performed Born-Oppenheimer molecular dynamics simulations and density functional th

52 Molecular dynamics simulations and density-functional me

53 Using molecular dynamics simulations and electrophysiology mea

54 report for the first time, using a combined molecular dynamics simulations and experimental approach

55 Here, using molecular dynamics simulations and fluorescence experime

56 Here, by performing molecular dynamics simulations and free energy calculati

57 Here we show, using X-ray crystallography, molecular dynamics simulations and in vitro and in vivo

58 Using molecular dynamics simulations and Kirkwood-Buff theory

59 s elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion me

60 By combining atomistic molecular dynamics simulations and oocyte permeability a

61 e underlying mechanism is understood through molecular dynamics simulations and quantitative phonon-d

62 phase field crystal approach with classical molecular dynamics simulations and quantum-mechanical de

63 ors combine solid-state NMR measurements and molecular dynamics simulations and show that crystal pac

64 Here the authors combined NMR and molecular dynamics simulations and show that the RRM RNA

65 Molecular dynamics simulations and single-channel electr

66 chemical cross-linking method together with molecular dynamics simulations and single-molecule assay

67 We evaluated using molecular dynamics simulations and the free energy pertu

68 tal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments

69 tional models based on the X-ray structures, molecular-dynamics simulations and mutagenesis.

70 By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-ex

71 Single-channel lifetime experiments, molecular dynamics simulations, and a simple lipid compr

72 complemented with reaction pathway analyses, molecular dynamics simulations, and binding free-energy

73 etry (MS), electron microscopy, mutagenesis, molecular dynamics simulations, and computational dockin

74 By combining x-ray diffraction, molecular dynamics simulations, and electrochemistry, we

75 using fluorescence correlation spectroscopy, molecular dynamics simulations, and free energy calculat

76 rgy transfer (smFRET) experiments, classical molecular dynamics simulations, and nucleotide incorpora

77 f chemical synthesis, biological evaluation, molecular dynamics simulations, and protein mutagenesis,

78 tics of antibodies and their targets through molecular dynamics simulations (Antibodyomics7) and free

79 mutagenesis, ensemble-solution kinetics, and molecular dynamics simulation approaches, the structure

80 Coarse-grain molecular dynamics simulations are a key tool to that en

81 Coarse-grained molecular dynamics simulations are applied to explore th

82 Molecular dynamics simulations are conducted to investig

83 Ab initio calculations and molecular dynamics simulations are employed to clarify t

84 Here, atomistic molecular dynamics simulations are used to examine the s

85 scence emission spectroscopies together with molecular dynamics simulations are used to investigate t

86 Molecular dynamics simulations are well suited to charac

87 ements, accompanied by large-scale atomistic molecular dynamics simulations, are used for the first t

88 Recent progress in theory and molecular dynamics simulations as well as in ultrafast v

89 To make progress, molecular dynamics simulations based on atomic models of

90 on-based measurements and from force pulling molecular dynamics simulations, both in water.

91 Molecular dynamics simulations calculate the motion of e

92 energy perturbation method based on all-atom molecular dynamics simulations, can provide accurate the

93 Molecular dynamics simulations capture the correlation b

94 In this work, we combine molecular dynamics simulations capturing the kinetic ste

95 Molecular dynamics simulations carried out for the model

96 With a combination of molecular dynamics simulations, CD response calculations

97 Here, using all-atom molecular dynamics simulations combined with umbrella sa

98 Multiscale molecular dynamics simulations confirm proton transport

99 Molecular dynamics simulations confirm that catechol gro

100 Molecular dynamics simulations corroborate this finding

101 Our experimental and molecular dynamics simulation data suggested that the bu

102 Nuclear Magnetic Resonance measurements and Molecular Dynamics simulations, demonstrate that metal i

103 Molecular modeling and molecular-dynamics simulations demonstrated that the obs

104 sets and one additional small set derived by molecular dynamics simulations, demonstrated that the av

105 In agreement with the fluorescence data, molecular dynamics simulations display alternating solve

106 rformed extensive atomistic Replica Exchange Molecular Dynamics simulations, elucidating preferential

107 A molecular dynamics simulation experiment reported here a

108 Molecular dynamics simulations following docking of each

109 We performed molecular dynamics simulations for comparing the Ca2+-sa

110 ese five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and o

111 with single-channel experiments and extended molecular dynamics simulations from the companion articl

112 Systematic molecular dynamics simulations further provided molecula

113 bination of data-driven flexible docking and molecular dynamics simulations guided by previous experi

114 mplex and its isolated partners, comparative molecular dynamics simulations have been performed.

115 Neutron Brillouin scattering and molecular dynamics simulations have been used to investi

116 ference-NMR, isothermal microcalorimetry and molecular dynamics simulations have been used to study t

117 Ab initio molecular dynamics simulations have confirmed that water

118 The static DFT as well as ab initio molecular dynamics simulations have corroborated the exp

119 The molecular dynamics simulations helped to identify the im

120 flavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified singl

121 Here we investigate through molecular dynamics simulations how the formation of prec

122 rational spectroscopic probes with ab initio molecular dynamics simulations, hydrogen-bonding interac

123 NMR titration and Molecular Dynamics simulation identified the residues wi

124 Molecular dynamics simulations identified three novel in

125 e use Rosetta membrane modeling and all-atom molecular dynamics simulations in a membrane environment

126 Moreover, DFT calculations and molecular dynamics simulations in aqueous solvent mixtur

127 Elastic modulus of lignin, calculated by molecular dynamics simulations, increases initially with

128 ed between 6 and 298 K, which, combined with molecular dynamics simulations, indicate that inertial d

129 Molecular dynamics simulations indicated that unique P2X

130 A molecular dynamics simulation indicates that these two c

131 We report the results of atomistic molecular dynamics simulations informed by quantum-mecha

132 tructure of relaxors that is revealed by our molecular dynamics simulations is consistent with recent

133 ory, employing all-atom and explicit-solvent molecular dynamics simulations, is a rigorous physics-ba

134 Here we report a molecular dynamics simulation method to construct a comp

135 Through a combination of molecular dynamics simulations, mutagenesis, and A1-GpIb

136 ntial for translocation and enable the first molecular dynamics simulation of an 80S complex.

137 ach for electronic coupling calculation with molecular dynamics simulation of ET free energies.

138 A 2-mus constant-force, steered molecular dynamics simulation of the core force-sensing

139 h this possibility, extensive coarse-grained molecular dynamics simulations of a BR trimer in an expl

140 In both coarse-grained and all-atom molecular dynamics simulations of a dipalmitoylphosphati

141 Here, we present results from molecular dynamics simulations of a doubly acetylated hi

142 Through atomistic molecular dynamics simulations of a series of sequential

143 Molecular dynamics simulations of all three proteins wer

144 Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortiu

145 Molecular dynamics simulations of collagen structures in

146 pens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involv

147 cover the origins of asymmetry, we performed molecular dynamics simulations of dimer assembly.

148 Here, we report a series of molecular dynamics simulations of each SrtC enzyme with

149 Here, we performed molecular dynamics simulations of GLIC in the absence an

150 In this work, we use extensive molecular dynamics simulations of GluN1 and GluN2B ligan

151 oth classical and Born-Oppenheimer ab initio molecular dynamics simulations of glyoxal solvation at t

152 Microsecond molecular dynamics simulations of harzianin HK VI (HZ) i

153 ed Markov State Models (MSMs) from extensive molecular dynamics simulations of human DAT (hDAT) to ex

154 ook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-li

155 Here we report first-principles molecular dynamics simulations of MgSiO3 melt containing

156 ut close to half millisecond high-throughput molecular dynamics simulations of MOR bound to a classic

157 Here, we present the results of molecular dynamics simulations of one potential exhausti

158 We carry out extensive molecular dynamics simulations of perforated sheets with

159 imescale (400-500 micros aggregate) all-atom molecular dynamics simulations of protein kinase C-ligan

160 Molecular dynamics simulations of the dimeric hDAT indic

161 ad to aggregation and toxicity, we performed molecular dynamics simulations of the full-length RRM2 d

162 c acid relative to the metal; (1)H ENDOR and molecular dynamics simulations of the fully solvated SLO

163 used umbrella sampling and multimicrosecond molecular dynamics simulations of the GluA2 AMPA subtype

164 To test this, we used all-atom molecular dynamics simulations of the isolated TM domain

165 Here, all-atom molecular dynamics simulations of the mammalian StART-li

166 Explicit large-scale molecular dynamics simulations of the metamaterials with

167 in the Na2 site, by carrying out comparative molecular dynamics simulations of the models derived fro

168 Here, we have performed extensive molecular dynamics simulations of the passive permeation

169 We report atomically detailed molecular dynamics simulations of the permeation of the

170 Molecular dynamics simulations of the PR --> F intermedi

171 Here we use molecular dynamics simulations of the prototypical Pb(Mg

172 re, we perform high quality Born-Oppenheimer molecular dynamics simulations of the reaction mechanism

173 Coarse-grained molecular dynamics simulations of the stripping pathway

174 Explicitly solvated, all-atom molecular dynamics simulations of the three complexes (t

175 We performed 195 mus of all-atom, unbiased molecular dynamics simulations of the TREK-2 channel to

176 ificance of this novel variant, we performed molecular dynamics simulations of the wild type and p.P8

177 ssociated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphoryl

178 Molecular dynamics simulations of ubiquitin in water/gly

179 re authors perform classical and accelerated molecular dynamics simulations of vacancy-mediated catio

180 eport results from classical and accelerated molecular dynamics simulations of vacancy-mediated catio

181 Atomistic molecular dynamics simulations of wild type and QUAD ops

182 Kinetics and molecular dynamics simulations on several GalNAc-T2 flex

183 d H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as

184 We conducted quasi-classical direct molecular dynamics simulations on the phosphoric acid-ca

185 h a large effect, we carried out a series of molecular dynamics simulations on the polymers to obtain

186 In conjunction with molecular dynamics simulations, our method can identify

187 In molecular dynamics simulations, PGC1alpha induced correl

188 Molecular dynamics simulation predicted random movements

189 Molecular dynamics simulations predicted that R60A prefe

190 Results of molecular dynamics simulations provide insight into how

191 tion process by crystallography and unguided molecular dynamics simulations, providing an atomic-leve

192 Molecular dynamics simulations qualitatively support the

193 We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRaine

194 First-principles nonadiabatic quantum molecular dynamics simulations reproduce the observed ul

195 Molecular dynamics simulation results show that no matte

196 In vitro experiments and molecular dynamics simulations reveal distinct physical

197 Consistent with this, molecular dynamics simulations reveal that increases in

198 Molecular dynamics simulations reveal that Met(73)influe

199 Our molecular dynamics simulations reveal that multiple grap

200 Finally, molecular dynamics simulations reveal that TFAM/LSP comp

201 Molecular dynamics simulations reveal that this material

202 Molecular dynamics simulations reveal the importance of

203 Molecular dynamics simulations reveal the initial distri

204 rvations, combined with large-scale reactive molecular dynamics simulations, reveal the details of th

205 Molecular dynamics simulations revealed a novel intercal

206 Molecular dynamics simulations revealed an interaction o

207 Molecular dynamics simulations revealed that the catalyt

208 Molecular dynamics simulations revealed that these ligan

209 Molecular dynamics simulations revealed the particular r

210 3.5-mus molecular dynamics simulations show 66 +/- 2% dC16:1 in

211 O-adsorbed Ni(110) surface, Born-Oppenheimer molecular dynamics simulations show that direct impact o

212 Chemical footprinting and molecular dynamics simulations show that each ribosomal

213 Molecular dynamics simulations show that the ability of

214 gle channel analysis, mutational studies and molecular dynamics simulations show that the difference

215 Ab intio molecular dynamics simulations show that the electrical

216 Our extensive spectroscopic studies and molecular-dynamics simulations show that the proteins' f

217 Molecular dynamics simulations showed a stronger MA-bila

218 Here, we perform molecular dynamics simulations showing the epimerized he

219 , we performed comparative microsecond-scale molecular dynamics simulations starting from the inactiv

220 Moreover our NMR, mutagenesis and molecular dynamics simulation studies defined the sequen

221 ion of virus resistance, HA interaction, and molecular dynamics simulation studies elucidated the bin

222 ry, electrophysiology, antiviral assays, and molecular dynamics simulations suggest stronger binding

223 Steered molecular dynamics simulations suggest that a likely mec

224 Free energy scaling analysis and molecular dynamics simulations suggest that ion pairing

225 Molecular dynamics simulations suggest that these altern

226 Ab initio molecular dynamics simulations suggest the formation occ

227 Molecular dynamics simulations suggested a reduced bindi

228 Molecular dynamics simulations suggested that detachment

229 Molecular dynamics simulations suggested that the pathog

230 Atomistic molecular dynamics simulations support a mechanism by wh

231 idal assays, electron microscopy images, and molecular dynamics simulations support the proposed mech

232 Molecular dynamics simulations supported the formation o

233 Using two distinct molecular dynamics simulation techniques, we have obtain

234 In this work, we report multiscale reactive molecular dynamics simulations that characterize the fre

235 parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quan

236 ttering with density functional theory-based molecular dynamics simulations that the structure of the

237 Interestingly, as shown by molecular dynamics simulation, the protein displays dist

238 In molecular dynamics simulations, the side chains of resid

239 through isothermal titration calorimetry and molecular-dynamics simulation, the effect of several cli

240 g delivery and refractory materials, and use molecular dynamics simulation to investigate its loading

241 Here, we use molecular dynamics simulations to analyze the binding an

242 rystalline electrolyte, we apply large-scale molecular dynamics simulations to analyze the ionic tran

243 Here, we use high-throughput coarse-grained molecular dynamics simulations to characterize MscL gati

244 used double electron-electron resonance and molecular dynamics simulations to describe the ATP- and

245 f relaxation dispersion NMR spectroscopy and molecular dynamics simulations to determine ensembles of

246 Here we employ molecular dynamics simulations to determine whether othe

247 ive mass spectrometric glycan sequencing and molecular dynamics simulations to elucidate the substitu

248 ion microscopy, atomic force microscopy, and molecular dynamics simulations to examine H-NS/DNA inter

249 d quantitative spatial imaging and atomistic molecular dynamics simulations to examine molecular deta

250 We use molecular dynamics simulations to examine the binding mo

251 e of this region in Hsp70 allostery, we used molecular dynamics simulations to explore the conformati

252 5-gliadins were highlighted after performing molecular dynamics simulations to heat the proteins from

253 y Raman spectroscopy, mass spectrometry, and molecular dynamics simulations to identify the time-depe

254 In this work, we use large-scale Accelerated Molecular Dynamics simulations to investigate small (N =

255 quid-jet X-ray photoelectron experiments and molecular dynamics simulations to investigate the behavi

256 Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecu

257 In this communication, we used all-atom molecular dynamics simulations to investigate the specif

258 We used molecular dynamics simulations to predict an AMPA recept

259 We use molecular dynamics simulations to provide atomic-resolut

260 Here, we use extensive molecular dynamics simulations to reconcile recent singl

261 We use molecular dynamics simulations to resolve the molecular

262 se transition networks derived from all-atom molecular dynamics simulations to show that the oligomer

263 e combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformation

264 two-dimensional vibrational spectroscopy and molecular dynamics simulations to study the dynamics of

265 Here we apply extensive molecular dynamics simulations to study the folding of H

266 n function experiments, and first-principles molecular dynamics simulations to study the melting phen

267 coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translo

268 eaching/activation approaches, and atomistic molecular dynamics simulations to uncover the molecular

269 asurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single

270 OpenMM is a molecular dynamics simulation toolkit with a unique focu

271 H2, H3, and H4) by extensive explicit-water molecular dynamics simulations (total simulated time > 3

272 y, which, combined with EPR spectroscopy and molecular dynamics simulations, uncovers a novel regulat

273 Molecular-dynamics simulation was used to evaluate the e

274 Using cell biology and molecular dynamics simulations, we aimed to define the u

275 Based on molecular dynamics simulations, we argue that this behav

276 ngle X-ray scattering, NMR spectroscopy, and molecular dynamics simulations, we characterized the dyn

277 Using all-atom molecular dynamics simulations, we characterized the mol

278 By using state-of-the-art molecular dynamics simulations, we decipher the key elem

279 oscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that dist

280 e construction of hybrid PorB types and PorB molecular dynamics simulations, we demonstrate that loop

281 Using molecular dynamics simulations, we have identified other

282 Combined with transport assays and molecular dynamics simulations, we propose a novel mecha

283 Using molecular dynamics simulations, we reveal novel inter-re

284 nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggr

285 By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA-SP1 t

286 tropy, electron cryomicroscopy, and all-atom molecular dynamics simulations, we show that S3D cofilin

287 Massive all-atom molecular dynamics simulations were conducted across a d

288 functional theory computations and long-time molecular dynamics simulations were employed to accurate

289 In this study, molecular dynamics simulations were employed to compare

290 Molecular dynamics simulations were used to calculate th

291 Molecular dynamics simulations were used to probe the st

292 Steered molecular dynamics simulations were used to quantify the

293 These experiments are corroborated by molecular dynamics simulations which show that supersoni

294 of this ligand recognition are addressed by molecular dynamics simulations, which reveal significant

295 We perform the first molecular dynamics simulation with a machine-learned den

296 d a multidisciplinary approach that combines molecular dynamics simulation with interfacial x-ray sca

297 In this study, we used all-atom molecular dynamics simulations with both enhanced and bi

298 By comparing the results of atomistic molecular dynamics simulations with experimental X-ray s

299 Molecular dynamics simulations with reagent excitation b

300 aguin-Landau-Vervey-Overbeek theory, whereas molecular-dynamics simulations with combined atomistic a