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

1 process as elucidated by solid-state NMR and molecular dynamics simulation.

2 ace are differentiable, backed with all-atom molecular dynamics simulations.

3 e transporter show decreased k(off) rates in molecular dynamics simulations.

4 nergy of translocation for the two drugs via molecular dynamics simulations.

5 and theoretical predictions were made using molecular dynamics simulations.

6 f nucleosomes that mediate Oct4 binding from molecular dynamics simulations.

7 ture was confirmed using NOE restraint-based molecular dynamics simulations.

8 rmations is first generated, typically using molecular dynamics simulations.

9 c surface plasmon resonance measurements and molecular dynamics simulations.

10 spectroscopy, and all-atom explicit solvent molecular dynamics simulations.

11 uterium exchange mass spectrometry data with molecular dynamics simulations.

12 eptides containing either SIM2 or SIM3 using molecular dynamics simulations.

13 onents by energy landscape determination and molecular dynamics simulations.

14 Young's modulus of nucleosomes from all-atom molecular dynamics simulations.

15 us size predictions based on theoretical and molecular dynamics simulations.

16 x with the full beta2R agonist BI-167107 for molecular dynamics simulations.

17 Abeta, as confirmed by extended (1-mus-long) molecular dynamics simulations.

18 y perturbation techniques based on atomistic molecular dynamics simulations.

19 Ras4B in 1.45-ms aggregate time of atomistic molecular dynamics simulations.

20 KRAS:RBD-CRD:membrane complex has relied on molecular dynamics simulations.

21 sition/stripping is revealed using ab initio molecular dynamics simulations.

22 igid nature of GB1 and with predictions from molecular dynamics simulations.

23 ation, statistical fragmentation methods and molecular dynamics simulations.

24 o milliseconds of all-atom, explicit-solvent molecular dynamics simulations.

25 eral X-ray structures, NMR binding data, and molecular dynamics simulations.

26 spectroscopy, stopped-flow experiments, and molecular dynamics simulations.

27 stitution, amino acid sequence analysis, and molecular dynamics simulations.

28 by magic-angle spinning NMR and data-guided molecular dynamics simulations.

29 , the stretched exponential decay model, and molecular dynamics simulations.

30 nd are complemented by electrophysiology and molecular dynamics simulations.

31 tudy these questions using enhanced sampling molecular dynamics simulations.

32 e studies, and theoretically using classical molecular dynamics simulations.

33 ansient infrared spectroscopy accompanied by molecular dynamics simulations.

34 mented these experimental data with all-atom molecular dynamics simulations.

35 large water box of standard all-atom steered molecular dynamics simulations.

36 00)(+) ion, consistent with our results from molecular dynamics simulations.

37 re-orient during catalysis, as supported by molecular dynamics simulations.

38 These distributions were confirmed by molecular dynamics simulations.

39 ry ion mass spectrometry in combination with molecular dynamics simulations.

40 temperature measurements were correlated to molecular dynamics simulations.

41 study, we have performed long-time atomistic molecular dynamics simulations (1 mus for each system) f

42 -vSFG) spectroscopy with ab initio DFT-based molecular dynamics simulations (AIMD/DFT-MD) to get dire

43 Steered molecular dynamics simulations allowed us to rationalize

44 Molecular dynamics simulations also revealed the importa

45 Our molecular dynamics simulations also suggest that membran

46 e mechanism is comprehensively elucidated by molecular dynamics simulation and density functional the

47 Molecular dynamics simulation and fluorescence resonance

48 In this work, aided by molecular dynamics simulation and modeling, a pertussis-

49 Molecular dynamics simulation and normal mode analysis m

50 the formation of transient fusion stalks in molecular dynamics simulations and a coexisting sponge p

51 entrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage as

52 filament polymerization and nucleation with molecular dynamics simulations and a previously establis

53 We describe extensive molecular dynamics simulations and analysis on physiolog

54 etween the ATP and RNA binding pockets using molecular dynamics simulations and enzymatic characteriz

55 Our method is based on molecular dynamics simulations and free energy calculati

56 hybrid quantum mechanics-molecular mechanics molecular dynamics simulations and free energy calculati

57 rbene binding to G-quadruplexes, we employed molecular dynamics simulations and free energy simulatio

58 e combine our SAXS and SANS experiments with molecular dynamics simulations and previously obtained N

59 copy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-chemical calc

60 e combined fast perfusion electrophysiology, molecular dynamics simulations and state-dependent non-c

61 Molecular dynamics simulations and studies in cells reve

62 s were studied using reverse non-equilibrium molecular dynamics simulations and the transient pump-pr

63 Using molecular dynamics simulations and transferable force fi

64 Structural analysis using molecular dynamics simulations and well-tempered metadyn

65 to hydrophobic substrate permeation through molecular-dynamics simulations and by characteristic NMR

66 mmuno-infrared sensor measurements, docking, molecular dynamics simulations, and ab initio calculatio

67 exchange mass spectrometry, complemented by molecular dynamics simulations, and bacterial susceptibi

68 ination of time-lapse X-ray crystallography, molecular dynamics simulations, and DNA enzymology on th

69 Using NMR spectroscopy, molecular dynamics simulations, and isothermal titration

70 Homology modeling, molecular dynamics simulations, and lysosomal localizati

71 hly studied using fluorescence spectroscopy, molecular dynamics simulations, and mixed quantum mechan

72 wever, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy,

73 Using NMR chemical shift analyses, molecular dynamics simulations, and site-directed mutage

74 nctional state assignments were validated by molecular dynamics simulations, and the observed permeat

75 AS4b, we used complementary experimental and molecular dynamics simulation approaches to reveal a det

76 Here, using molecular dynamics simulation approaches, we found that

77 Here, experimental observations and molecular dynamics simulations are employed to identify

78 Microsecond-long all-atom molecular dynamics simulations are then calculated for h

79 emical potential Grand Canonical Monte Carlo/molecular dynamics simulations are used to capture the e

80 changes pose unique challenges to classical molecular dynamics simulations, as well as some possible

81 Atomistic modeling and molecular dynamics simulations based on a detailed energ

82 Herein, molecular dynamics simulations based on a recently solve

83 Enhanced sampling molecular dynamics simulations based on either force fie

84 Using structure-based and explicit solvent molecular dynamics simulations based on recent cryo-elec

85 se-grained structural modeling, and all-atom molecular dynamics simulations-based refinement, and (ii

86 so, we show that piecewise all-atom steered molecular dynamics simulations can provide novel atomic

87 Overlapping large-scale molecular dynamics simulations capture the atomistic det

88 s studied via classical and first-principles molecular dynamics simulations combined with free-energy

89 Previous molecular dynamics simulations conducted by our group ha

90 Molecular dynamics simulations confirm the existence of

91 andidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stability of

92 Molecular dynamics simulations demonstrated that the p.Q

93 g of crystal structures into the density and molecular dynamics simulations, describes interaction in

94 We have performed a large set of all-atom molecular dynamics simulations employing the highly mobi

95 We have employed protein modeling, molecular dynamics simulations, evolutionary mapping, an

96 Here, we perform molecular dynamics simulations for Caulobacter crescentu

97 Our three-dimensional molecular dynamics simulations, fully incorporating fric

98 10-mus molecular dynamics simulations further correlated Omega-

99 Molecular dynamics simulations further identify two hots

100 Molecular dynamics simulations gave information on the g

101 Molecular dynamics simulations give an insight into the

102 Many molecular dynamics simulations have investigated phase s

103 , chromatin immunoprecipitation, docking and molecular dynamics simulations, human unfolded protein r

104 Molecular modeling and molecular dynamics simulations identify models for these

105 These structures and accompanying molecular dynamics simulations identify two metal-bindin

106 changes during a 10-mus-timescale atomistic molecular dynamics simulation in an explicit membrane en

107 tion by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent.

108 imerization and dissociation using atomistic molecular-dynamics simulation in explicit water.

109 By combining X-ray crystallography with molecular dynamics simulations, in vitro kinetic studies

110 Molecular dynamics simulations indicate different contac

111 Molecular dynamics simulations indicate several conforma

112 Molecular dynamics simulations indicate that hardening i

113 At the air-water interface, Born-Oppenheimer molecular dynamics simulations indicate that the cycload

114 All-atom molecular dynamics simulations indicate that the FUS-LC-

115 Atomistic molecular dynamics simulations indicate this is because

116 Molecular dynamics simulations indicated that F302L alte

117 th various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxep

118 Molecular dynamics simulations indicated that the onset

119 edly, protein crystal structure analysis and molecular dynamics simulations indicated widespread redo

120 Molecular dynamics simulation indicates that, in the abs

121 ingle-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe bin

122 Molecular dynamics simulation infers that facet-dependen

123 tion-resolved fluorescence spectroscopy with molecular dynamics simulations is shown to be a powerful

124 Together with all-atom molecular dynamics simulations, it is shown that Cx46/50

125 0.25 +/- 0.05) and those calculated from the molecular dynamics simulations (<E(FRET)(MD)> = 0.18 +/-

126 onfocal laser scanning microscopy (CLSM) and molecular dynamics simulations (MDSs) to analyze how ann

127 template to create an inactive apo-AT1R via molecular dynamics simulation (n = 3).

128 Here, we present a direct method based on molecular dynamics simulation of nanostructured surfaces

129 Indeed, a molecular dynamics simulation of the CENP-A 601 NCP conf

130 a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD constru

131 Using molecular dynamics simulations of a model mixture of ski

132 Finally, molecular dynamics simulations of a model system for the

133 results of submillisecond adaptive sampling molecular dynamics simulations of a predicted methadone-

134 This is achieved by means of extensive molecular dynamics simulations of a simple polymer model

135 r Waals terms dictated by cosolvent all-atom molecular dynamics simulations of antibody variable regi

136 we have carried out 45.5 mus of equilibrium molecular dynamics simulations of BamA with and without

137 We present molecular dynamics simulations of chromatosomes with the

138 Molecular dynamics simulations of cone GAFab revealed di

139 s and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subty

140 Molecular dynamics simulations of different Orai variant

141 Molecular dynamics simulations of DOM model compounds ca

142 structures of both glycoproteins to generate molecular dynamics simulations of each glycoprotein both

143 ) simulation method that enables microsecond molecular dynamics simulations of full-length antibodies

144 We used molecular dynamics simulations of fusion between a full-

145 Molecular dynamics simulations of KPC:ceftazidime acyl-e

146 ere, we report the results of coarse-grained molecular dynamics simulations of monomeric and filament

147 e report first principles (FP) and classical molecular dynamics simulations of NaCl in the dilute lim

148 Atomistic molecular dynamics simulations of P2 on model membrane s

149 Molecular dynamics simulations of post-powerstroke myosi

150 Molecular dynamics simulations of post-powerstroke myosi

151 Molecular dynamics simulations of single NCs confirm tha

152 Molecular dynamics simulations of such ions bearing intr

153 This observation was further supported by molecular dynamics simulations of the ch28/11-glycan com

154 Results of molecular dynamics simulations of the DAD2(N242I) struct

155 ved Trp207 with solvent in multi-microsecond molecular dynamics simulations of the Dio3 thioredoxin(T

156 mycin, we employed all-atom explicit-solvent molecular dynamics simulations of the full ribosome-EF-T

157 We ran 800-ns long molecular dynamics simulations of the PRD using an expli

158 The molecular dynamics simulations of the SMC-kleisin protei

159 Steered molecular dynamics simulations of these models suggest c

160 re we detail a combination of densimetry and molecular dynamics simulations of three cavitands, coupl

161 ded for intrinsically disordered proteins in molecular dynamics simulations of three proteins differi

162 Molecular dynamics simulations of TREK1 in the presence

163 ing three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter

164 ected to torques and stretching forces using molecular dynamics simulations on an atomistically resol

165 Our all-atomic molecular dynamics simulations on complete transmembrane

166 ensemble, we performed Gaussian accelerated molecular dynamics simulations on eight BAK1 mod-forms i

167 All atom molecular dynamics simulations on EMB in its nucleotide-

168 Together with molecular dynamics simulations, our analyses suggest two

169 The results of molecular dynamics simulations performed on ganglioside-

170 Discontinuous molecular dynamics simulations predict that CATCH(+) and

171 Molecular dynamics simulations predicted that tyrosine n

172 utational chemistry and quantum mechanics by molecular dynamics simulation program before chemical sy

173 Analyses of cocrystal structures and molecular dynamics simulations provide insights into opt

174 X-ray crystallography and molecular dynamics simulations provide strong evidence t

175 Finally, molecular dynamics simulations provided a detailed struc

176 Molecular dynamics simulations provided insight into the

177 Protein-protein docking and molecular dynamics simulations provided models for the S

178 Molecular dynamics simulations provided structural expla

179 Extensive molecular dynamics simulations provided useful mechanist

180 In silico modeling by molecular dynamics simulations provides atomic-level str

181 ze with conformational changes inferred from molecular dynamics simulations, providing a paradigm for

182 Molecular dynamics simulations rationalize the molecular

183 Molecular dynamics simulations reinforce the experimenta

184 Molecular dynamics simulation results indicate high conf

185 hese structures, along with crosslinking and molecular dynamics simulation results, suggest how a pol

186 Molecular dynamics simulations reveal compensatory roles

187 Coarse-grained molecular dynamics simulations reveal that the transloco

188 In situ Raman spectroscopy and molecular dynamics simulations reveal the synergistic in

189 Full-scale molecular-dynamics simulations reveal that the grafted s

190 Here, neutron scattering and molecular-dynamics simulations reveal the temperature-de

191 Molecular dynamics simulation revealed that the R1060C m

192 Molecular dynamics simulations revealed that at low pH,

193 gen-deuterium exchange mass spectrometry and molecular dynamics simulations revealed that glycosylati

194 lectron microscopy multivariate analysis and molecular dynamics simulations revealed that interaction

195 Molecular dynamics simulations revealed that the p.Arg29

196 Molecular dynamics simulations revealed that the x-ray s

197 V-1 MA, using the surface-mapping method and molecular dynamics simulations, revealed that the residu

198 Atomistic molecular dynamics simulation reveals short-range polar

199 Molecular dynamics simulations show a selective enrichme

200 Molecular dynamics simulations show that an understandin

201 Molecular dynamics simulations show that NO(3) (-) parti

202 Molecular dynamics simulations show that the regulatory

203 Molecular dynamics simulations show that this supramolec

204 Indeed, our molecular dynamics simulations show the TnT1 component i

205 Ab initio molecular dynamics simulations show these high conductiv

206 Molecular dynamics simulation showed that indole alloste

207 Microsecond-scale atomistic molecular dynamics simulations showed that 4F interactio

208 Explicit-atom molecular dynamics simulations showed that minor groove

209 Molecular dynamics simulations showed that specific muta

210 Analytical viscometry coupled with molecular dynamics simulations showed that the A277V mut

211 Here, we use molecular dynamics simulations showing sequence differen

212 In molecular dynamics simulations, SS-RJW100 attenuates int

213 Atomistic molecular dynamics simulations starting from SAS-6 head

214 Molecular dynamics simulation studies confirm that the c

215 We present a molecular dynamics simulation study on the binding mecha

216 Experiment and molecular dynamics simulation suggest that the stabiliza

217 Molecular dynamics simulations suggest a close proximity

218 In turn, molecular dynamics simulations suggest altered VSD expos

219 Molecular dynamics simulations suggest that AimB binds M

220 Furthermore, molecular dynamics simulations suggest that lipids can f

221 Finally, molecular dynamics simulations suggest that modulation o

222 Molecular dynamics simulations suggest that the anionic

223 Molecular dynamics simulations suggest that the opening

224 Molecular dynamics simulations suggested that SvBAHD05 i

225 linositol 4,5-bisphosphate (PIP(2)), and our molecular dynamics simulation suggests PIP(2) interactio

226 Moreover, molecular dynamics simulation suggests that the central

227 Molecular dynamics simulations support the two-metal ion

228 gated experimentally and are correlated with molecular dynamics simulations that reveal the changes o

229 To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding

230 solved by X-ray crystallography, and, using molecular dynamics simulations, the dynamics of VCBC hav

231 In this study, we applied ab initio molecular dynamics simulation to investigate the structu

232 We used coarse-grained molecular dynamics simulations to characterize the globa

233 ansmission electron microscopy combined with molecular dynamics simulations to demonstrate that fivef

234 We use experimental approaches and molecular dynamics simulations to describe the underlyin

235 Here, we use extensive atomic-level molecular dynamics simulations to determine how arrestin

236 We use extensive molecular dynamics simulations to determine three-dimens

237 o-electron tomography, network analysis, and molecular dynamics simulations to directly measure the m

238 mploy single-molecule force spectroscopy and molecular dynamics simulations to dissect the behavior o

239 This study aimed to use molecular dynamics simulations to elucidate how Ca(2+)-b

240 We used biochemical experiments and molecular dynamics simulations to elucidate the selectiv

241 ed a piecewise approach for all-atom steered molecular dynamics simulations to examine specific secon

242 We also use finite-temperature molecular dynamics simulations to explore the coexistenc

243 y high-pressure powder X-ray diffraction and molecular dynamics simulations to gain insight into the

244 docking and the complexes were relaxed with molecular dynamics simulations to investigate the intera

245 t, two-dimensional infrared spectroscopy and molecular dynamics simulations to measure the effect of

246 Here in this work we deployed molecular dynamics simulations to optimise the selection

247 Here we use density functional theory-based molecular dynamics simulations to predict the electrical

248 Here, we use molecular dynamics simulations to probe conformations sa

249 We employ here microsecond molecular dynamics simulations to probe the dynamics of

250 In this study, we use fully atomistic molecular dynamics simulations to scrutinize the structu

251 Herein we have performed Born-Oppenheimer molecular dynamics simulations to study the behavior of

252 us complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechan

253 cence resonance energy transfer (smFRET) and molecular dynamics simulations to study the mechanism of

254 Here, we performed molecular dynamics simulations to study two bimolecular

255 In this study, we used molecular dynamics simulations to unravel the molecular

256 Molecular dynamics simulations, together with surface ma

257 dynamics and nanopore measurements, we apply molecular dynamics simulations using a simplified "struc

258 Herein, we employ classical molecular dynamics simulations using the Drude oscillato

259 the binding process in atomistic detail with molecular dynamics simulations using trypsin and its inh

260 Here, using coarse-grained molecular dynamics simulations validated against atomist

261 Using molecular dynamics simulation, we demonstrate that the p

262 In our study, using molecular dynamics simulation, we have investigated the

263 a combined approach of cryo-EM and atomistic molecular dynamics simulation, we present the structure

264 ies, site-directed mutagenesis, and advanced molecular dynamics simulations, we also find that BAK ac

265 ella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen so

266 By coupling our model with molecular dynamics simulations, we can predict the criti

267 of isotope-edited infrared spectroscopy and molecular dynamics simulations, we characterize the effe

268 Supported by molecular dynamics simulations, we conclude that the E34

269 By combining NMR chemical shifts with molecular dynamics simulations, we confirmed that confor

270 Using native mass spectrometry and molecular dynamics simulations, we deduce the length of

271 Using X-ray crystallography and molecular dynamics simulations, we determined the Y269 r

272 ling of the complete transition path for our molecular dynamics simulations, we developed a "gizmo" p

273 Using coarse-grained molecular dynamics simulations, we explore the lipid-pro

274 From extended molecular dynamics simulations, we find that both nucleo

275 Using nuclear magnetic resonance data and molecular dynamics simulations, we generated the first a

276 Using molecular dynamics simulations, we go on to identify uni

277 By applying molecular dynamics simulations, we have determined the p

278 east functional complementation and extended molecular dynamics simulations, we reveal a unique two-l

279 Using data from all-atom molecular dynamics simulations, we reveal these differen

280 ning FTIR and UV-Vis spectroscopy along with molecular dynamics simulations, we show here for the wid

281 g structural biology, functional assays, and molecular dynamics simulations, we show how the barrel p

282 Using coarse-grained molecular dynamics simulations, we show that lipopolysac

283 bation, corona surface characterization, and molecular dynamics simulations, we show that the molecul

284 g a combination of in vitro assays, NMR, and molecular dynamics simulations, we show that these small

285 Using molecular dynamics simulations, we studied how modified

286 r structure-membrane activity relationships, molecular dynamics simulations were carried out.

287 Modelling and molecular dynamics simulations were fully consistent wit

288 Molecular dynamics simulations were performed with four

289 rbonic anhydrases, and homology modeling and molecular dynamics simulations were performed.

290 Extensive molecular dynamics simulations were undertaken to elucid

291 In the present study, molecular dynamics simulations were used in tandem with

292 h we observed failed substrate delivery in a molecular dynamics simulation where the energized ion st

293 acellular loops, predicted using docking and molecular dynamics simulation with newly constructed mA(

294 alpha7 activation, we ran triplicate 500-ns molecular dynamics simulations with an alpha7 extracellu

295 amics of the UUCG RNA stem-loop by combining molecular dynamics simulations with experimental data.

296 dary structure ensemble produced by all-atom molecular dynamics simulations with implicit solvent.

297 By combining molecular dynamics simulations with kinetic modeling, we

298 bles connecting the picosecond timescales of molecular dynamics simulations with the millisecond time

299 3D11 binding to P. berghei CSP (PbCSP) using molecular dynamics simulations, X-ray crystallography, a

300 ly determined high resolution structures and molecular dynamics simulations, yields a molecular model