ライフサイエンスコーパス: molecular dynamics

1 ng tunneling microscopy (STM), and ab initio molecular dynamics.

2 ng tunneling microscopy and theoretically by molecular dynamics.

3 ntaining lipid bilayer, using coarse-grained molecular dynamics.

4 or a robust dimension and model reduction in molecular dynamics.

5 Ab initio molecular dynamics (AIMD) simulations and molecular beam

6 O4), and has also been verified by ab initio molecular dynamics (AIMD) simulations.

7 Ab initio molecular dynamics (AIMD)-informed EXAFS analysis was em

8 ontrol any dynamics engine, such as standard molecular dynamics and cell-modeling packages.

9 Molecular dynamics and circular dichroism revealed an am

10 We apply all-atom molecular dynamics and coarse-grained finite element mod

11 host and the guest is confirmed by combined molecular dynamics and density functional theory calcula

12 Molecular dynamics and finite elements simulations are u

13 Molecular dynamics and free-energy simulations confirm d

14 We use classical molecular dynamics and hybrid quantum mechanics/molecula

15 bserved effect of temperature on the lipids' molecular dynamics and inducing an ordering effect that

16 nic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages.

17 Molecular dynamics and mutational analyses showed that a

18 A new crystal structure, together with molecular dynamics and NMR studies, has revealed how the

19 ection of local minima that are sampled with molecular dynamics and QM geometry optimization enabling

20 electrochemistry, site-directed mutagenesis, molecular dynamics and quantum chemical calculations to

21 opy of the S=O stretching mode combined with molecular dynamics and quantum chemistry models were use

22 Using structural analysis, molecular dynamics, and biochemistry, we show that TA in

23 Here, we present a molecular dynamics approach to identify and quantitative

24 By using a multiscale coarse-grained molecular dynamics approach, we show that, due to ionic

25 d complementary cell-based, biochemical, and molecular dynamics approaches, we propose a mechanism fo

26 Chemical cross-linking and molecular dynamics are consistent with this interaction

27 Structures calculated using classical molecular dynamics are in excellent agreement with the o

28 Born-Oppenheimer molecular dynamics (BOMD) simulation shows that, in the

29 Herein, Born-Oppenheimer molecular dynamics (BOMD) simulations examine the dynami

30 he basis of IR absorption spectroscopy, NMR, molecular dynamics calculations and X-ray diffraction ex

31 vidual NTs coupled with first-principles and molecular dynamics calculations demonstrate the unique p

32 We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing

33 In this work, discontinuous molecular dynamics combined with the PRIME20 force field

34 performed collective variable-based steered molecular dynamics (CVSMD) simulations starting with the

35 This is consistent with molecular dynamics data on excimer stability.

36 eport a novel method DynaSeq, which predicts molecular dynamics-derived ensembles of a more exhaustiv

37 , we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid a

38 To this end, we used steered molecular dynamics, electrophysiology, and kinetic model

39 Analysis of steered molecular dynamics experiments identified three transmem

40 n model of the RSV CA tubular assembly using molecular dynamics flexible fitting (MDFF) simulations.

41 ormance of free energy calculations based on molecular dynamics for the prediction of selectivity by

42 ampling regime, using a Gaussian-accelerated molecular dynamics (GaMD) methodology, which probes disp

43 quantitatively understand complex control of molecular dynamics in vivo.

44 Traditional molecular dynamics (MD) and replica-exchange MD (REMD) s

45 ned by extensive molecular modeling (MM) and molecular dynamics (MD) computations.

46 f human calcitonin through two complementary molecular dynamics (MD) methods, finding that human calc

47 force fields used to generate the underlying molecular dynamics (MD) simulation data.

48 pose, extensive (1)H NMR binding studies and molecular dynamics (MD) simulation experiments revealed

49 evidence from these studies is confirmed by molecular dynamics (MD) simulation in the range of atomi

50 ard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most w

51 Molecular dynamics (MD) simulations and far-infrared (fa

52 Molecular dynamics (MD) simulations are used to model ch

53 All-atom molecular dynamics (MD) simulations confirm that the ful

54 tein surface, we performed enhanced sampling molecular dynamics (MD) simulations of a model glycosyla

55 s are raising expectations on the quality of molecular dynamics (MD) simulations of DNA, as well as t

56 Comparisons of molecular dynamics (MD) simulations on the wild-type and

57 Preliminary molecular dynamics (MD) simulations revealed that the in

58 Molecular Dynamics (MD) simulations revealed the variati

59 Temperature-dependent Molecular Dynamics (MD) simulations show that apo-CaM ex

60 Molecular dynamics (MD) simulations suggest that LSD's s

61 We demonstrate via a series of molecular dynamics (MD) simulations that such a model is

62 Here we combine PELDOR experiments with molecular dynamics (MD) simulations to arrive at an atom

63 Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activat

64 In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state mo

65 trafast time-resolved infrared spectroscopy, molecular dynamics (MD) simulations, and spectral modeli

66 generated by our restraint-based strategy to molecular dynamics (MD) simulations, we revealed the con

67 ombining chemical force microscopy (CFM) and molecular dynamics (MD) simulations.

68 ux tension propagation theory, and extensive molecular dynamics (MD) simulations.

69 dent conformational dynamics of hPDI through molecular dynamics (MD) simulations.

70 um mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) study on wild-type and mutant st

71 In this paper, we use reactive molecular dynamics (MD) to simulate the scenario of a sh

72 rial-and-error calculations using restrained molecular dynamics (MD) with simulated annealing (SA).

73 stochastic or atomistic simulations, such as molecular dynamics (MD).

74 MgO in cement pore solution are simulated by molecular dynamics (MD).

75 -deuterium exchange MS (HDX-MS) methods, and molecular dynamics (MD).

76 turbation (FEP) coupled with lambda-exchange molecular dynamics method to calculate the binding free

77 rall stiffness, we introduced a coarse-grain molecular dynamics model of the axon membrane skeleton t

78 analysis coupled with molecular docking and molecular dynamics modeling revealed that MB-10 binds to

79 uine antiplasticizing effect of water on the molecular dynamics of a small-molecule glass former.

80 Here, we determine molecular dynamics of Env on the surface of individual H

81 ing designer-tailored pulses for controlling molecular dynamics of opsins in living tissue to selecti

82 le-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside

83 e Normal Mode-based geometric Simulation and Molecular Dynamics predict a general rigidification of t

84 cal reactions were studied with the reactive molecular dynamics (ReaxFF MD) simulations by using the

85 The model employs an atomistic (molecular dynamics) representation of a fraction of the

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

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

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

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

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

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

92 A molecular dynamics simulation experiment reported here a

93 NMR titration and Molecular Dynamics simulation identified the residues wi

94 A molecular dynamics simulation indicates that these two c

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

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

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

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

99 Molecular dynamics simulation predicted random movements

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

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

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

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

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

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

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

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

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

109 water spreading on hydrophobic surfaces via molecular dynamics simulation.

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

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

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

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

114 Molecular dynamics simulations and density-functional me

115 Using molecular dynamics simulations and electrophysiology mea

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

117 Here, using molecular dynamics simulations and fluorescence experime

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

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

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

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

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

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

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

125 Molecular dynamics simulations are conducted to investig

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

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

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

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

130 Molecular dynamics simulations calculate the motion of e

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

132 Molecular dynamics simulations carried out for the model

133 Multiscale molecular dynamics simulations confirm proton transport

134 Molecular dynamics simulations corroborate this finding

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

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

137 Systematic molecular dynamics simulations further provided molecula

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

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

140 Ab initio molecular dynamics simulations have confirmed that water

141 The molecular dynamics simulations helped to identify the im

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

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

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

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

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

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

148 Molecular dynamics simulations of collagen structures in

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

164 Coarse-grained molecular dynamics simulations of the stripping pathway

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

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

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

168 Molecular dynamics simulations of ubiquitin in water/gly

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

170 Atomistic molecular dynamics simulations of wild type and QUAD ops

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

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

173 Results of molecular dynamics simulations provide insight into how

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

175 In vitro experiments and molecular dynamics simulations reveal distinct physical

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

177 Our molecular dynamics simulations reveal that multiple grap

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

179 Molecular dynamics simulations reveal that this material

180 Molecular dynamics simulations reveal the initial distri

181 Molecular dynamics simulations revealed a novel intercal

182 Molecular dynamics simulations revealed an interaction o

183 Molecular dynamics simulations revealed that the catalyt

184 Molecular dynamics simulations revealed that these ligan

185 3.5-mus molecular dynamics simulations show 66 +/- 2% dC16:1 in

186 Chemical footprinting and molecular dynamics simulations show that each ribosomal

187 Molecular dynamics simulations show that the ability of

188 Ab intio molecular dynamics simulations show that the electrical

189 Molecular dynamics simulations showed a stronger MA-bila

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

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

192 Steered molecular dynamics simulations suggest that a likely mec

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

194 Ab initio molecular dynamics simulations suggest the formation occ

195 Molecular dynamics simulations suggested a reduced bindi

196 Molecular dynamics simulations suggested that detachment

197 Molecular dynamics simulations suggested that the pathog

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

199 Molecular dynamics simulations supported the formation o

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

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

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

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

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

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

206 Here we employ molecular dynamics simulations to determine whether othe

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

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

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

210 We use molecular dynamics simulations to examine the binding mo

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

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

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

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

215 We used molecular dynamics simulations to predict an AMPA recept

216 We use molecular dynamics simulations to provide atomic-resolut

217 We use molecular dynamics simulations to resolve the molecular

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

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

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

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

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

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

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

225 Molecular dynamics simulations were used to probe the st

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

227 Molecular dynamics simulations with reagent excitation b

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

246 In molecular dynamics simulations, PGC1alpha induced correl

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

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

249 In molecular dynamics simulations, the side chains of resid

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

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

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

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

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

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

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

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

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

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

260 the distortions observed in fully atomistic molecular dynamics simulations.

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

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

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

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

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

266 hese bilayer heights were investigated using molecular dynamics simulations.

267 ctures and investigated their stability with molecular dynamics simulations.

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

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

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

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

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

273 vibrational spectroscopy in combination with molecular dynamics simulations.

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

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

276 allosteric mechanism revealed by microsecond molecular dynamics simulations.

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

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

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

280 Additionally, all-atom steered molecular dynamics (SMD) simulations on homology models

281 atomic force microscopy (smAFM) and steered molecular dynamics (SMD) simulations.

282 Here, we present atomistic molecular dynamics studies of the closed-state, non-cond

283 riments, NMR analyses and quantum mechanical/molecular dynamics studies on human KMT-catalyzed methyl

284 Molecular dynamics studies revealed that ET between Trp(

285 insic fluorescence, limited proteolysis, and molecular dynamics studies suggest the protein may sampl

286 We have carried out free energy and molecular dynamics studies to determine the preferred co

287 A recent molecular dynamics study for deciphering the principles

288 Here we use advanced molecular dynamics techniques to shed light on these non

289 In this work, using coarse-grained molecular dynamics, the transmembrane domains (TMDs) of

290 This approach extends the resolution of molecular dynamics to >100-fold higher concentrations, e

291 ons were C-H...pi, which likely restrict the molecular dynamics to create aggregation-induced enhance

292 We then use molecular dynamics to study the microscopic properties o

293 Molecular dynamics trajectories of glycosylated Skp1 who

294 state model analysis to a 50-mus data set of molecular dynamics trajectories of the human dopamine tr

295 novel perturbation-response decomposition of molecular dynamics trajectories.

296 aging, electrical transport and atomic-scale molecular dynamics, we demonstrate that conductance vari

297 Within the framework of steered molecular dynamics, we develop three different adhesion

298 mulations with density functional theory and molecular dynamics, we show that the previously accepted

299 ich an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for

300 udies based on density functional theory and molecular dynamics, which show that the excess free ener