ライフサイエンスコーパス: molecular dynamics

1 adder segment of NS1 with extensive all atom molecular dynamics.

2 h applications to measure microviscosity and molecular dynamics.

3 lyzed by means of optical spectroscopies and molecular dynamics.

4 zed further by flexible fitting routines and molecular dynamics.

5 ked beam method and simulated using reactive molecular dynamics.

6 ture folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations and Monte Carl

7 results in combination with Born-Oppenheimer molecular dynamics, ab initio, and excited-state calcula

8 Results from ab initio molecular dynamics (AIMD) simulations and solid-phase ch

9 Ab initio molecular dynamics (AIMD) simulations confirm that alumi

10 Normal mode and molecular dynamics analyses indicate that these are like

11 Here we show, by combining non-equilibrium molecular dynamics and continuum simulations, that rigid

12 methodology, informed by explicitly solvated molecular dynamics and coupled cluster calculations, is

13 Supported by ab initio nonadiabatic molecular dynamics and diffraction simulations, our expe

14 Using extended molecular dynamics and enhanced sampling free-energy sim

15 We combined steered molecular dynamics and membrane protein-protein docking

16 Atomistic molecular dynamics and metadynamics simulations allow us

17 Molecular dynamics and metadynamics simulations provide

18 research, including methods such as steered molecular dynamics and metadynamics.

19 experiments in conjunction with large-scale molecular dynamics and physics-based discrete dislocatio

20 Molecular dynamics and protein-protein interaction studi

21 Using equilibrium molecular dynamics and umbrella sampling studies, we det

22 nd characterize selectivity mechanisms using molecular dynamics and X-ray crystallography.

23 e spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molecular mech

24 n microscopy, and density functional theory, molecular dynamics, and Monte Carlo calculations, and it

25 Electronic Structure Methods, Non-Adiabatic Molecular Dynamics, and Theoretical Spectroscopy represe

26 opy measurements establish the occurrence of molecular dynamics at the atomistic scale in cocrystals,

27 Molecular dynamics based folding simulations that rely o

28 et the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-ato

29 Herein we have performed Born-Oppenheimer molecular dynamics (BOMD) simulations and gas-phase quan

30 In this work, molecular dynamics calculations and an experimental proc

31 ined with ab initio electronic structure and molecular dynamics calculations of the excited- and grou

32 y in micelles and solved by using restrained molecular dynamics calculations.

33 stage of our understanding, assessing global molecular dynamics can prove to be inherently impractica

34 Density functional theory-molecular dynamics (DFT-MD) simulations of SCN(-) near t

35 ide compounds, via density-functional-theory molecular-dynamics (DFT-MD) simulations.

36 T1R polymorphisms were constructed using the molecular dynamics equilibrated apo-AT1R.

37 culations of Li-P-O/N crystals and ab initio molecular dynamics-generated amorphous LiPON models to u

38 that quenching is efficient due to anomalous molecular dynamics in the vicinity of the conical inters

39 CD and molecular dynamics indicate that the M8R mutation disrup

40 Molecular dynamics indicates that Aurora B S227 phosphor

41 ssure-volume-temperature ranges within which molecular dynamics is dominated by either complex H-bond

42 Using ab initio nonadiabatic molecular dynamics, it is demonstrated that alkalis brin

43 o our knowledge, locally distributed tension molecular dynamics (LDT-MD) simulation method that allow

44 This structure resulted from long molecular dynamics (MD) and metadynamics (metaMD) simula

45 Molecular dynamics (MD) is a powerful computational meth

46 In this study, molecular dynamics (MD) is used to study the binding bet

47 rier transform (DFT) analysis with ab initio molecular dynamics (MD) liquid-quench simulations.

48 ing a newly developed continuous constant pH molecular dynamics (MD) method and microsecond fixed-cha

49 to comparatively framed questions about the molecular dynamics (MD) of proteins can potentially enab

50 technology and computing power have rendered molecular dynamics (MD) simulation a powerful biophysica

51 Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statis

52 ctors were obtained as ratios of equilibrium Molecular Dynamics (MD) simulation data in physical unit

53 Herein, we show molecular dynamics (MD) simulation evidence of a previou

54 e revealed a specific Na(+) binding site and molecular dynamics (MD) simulation studies have supporte

55 These models were subjected to molecular dynamics (MD) simulation to determine the exte

56 Using all-atom molecular dynamics (MD) simulations and essential dynami

57 e-bound Dfg5*GPI-CWP complex is validated by molecular dynamics (MD) simulations and in vivo mutants

58 Molecular dynamics (MD) simulations are carried out to i

59 Molecular dynamics (MD) simulations can provide such inf

60 e multimicrosecond time scale using all-atom molecular dynamics (MD) simulations in an explicit lipid

61 face plasmon resonance characterization, and molecular dynamics (MD) simulations initiated from Roset

62 Here, molecular dynamics (MD) simulations of an 800 000 atom m

63 lighted by correcting "on the fly" DFT-based molecular dynamics (MD) simulations of resorcinol (C(6)H

64 investigate using 20 independent equilibrium molecular dynamics (MD) simulations over a total of 1 mu

65 Molecular dynamics (MD) simulations prove the ion pair a

66 Molecular Dynamics (MD) simulations seek to provide atom

67 We used molecular dynamics (MD) simulations to characterize the

68 tomic force microscopy (HS-AFM) and all-atom molecular dynamics (MD) simulations to study the behavio

69 ST2) as an example, we performed microsecond molecular dynamics (MD) simulations to study the conform

70 Here, we compared different nonequilibrium molecular dynamics (MD) simulations to study unfolding o

71 nance (NMR), neutron reflectometry (NR), and molecular dynamics (MD) simulations were employed to stu

72 Here, molecular dynamics (MD) simulations were performed toget

73 The study demonstrated that long timescale molecular dynamics (MD) simulations with a UGT2B7 homolo

74 mined partition coefficient was validated by molecular dynamics (MD) simulations with showing a stabi

75 hat is addressed here using a combination of molecular dynamics (MD) simulations, quantum mechanical/

76 Using molecular dynamics (MD) simulations, we discovered that

77 Employing all-atom molecular dynamics (MD) simulations, we established that

78 e deuterium NMR ((2)H NMR) spectroscopy, and molecular dynamics (MD) simulations-we report that chole

79 bacterium Thermotoga maritima using all-atom molecular dynamics (MD) simulations.

80 ng, and kinetic analyses, and long-timescale molecular dynamics (MD) simulations.

81 ions using in vitro fluorescence methods and molecular dynamics (MD) simulations.

82 mational transitions which can be studied by molecular dynamics (MD) simulations.

83 lorimetry (ITC), molecular docking (DC), and molecular dynamics (MD) were used to characterize NG-LF

84 hannel structure, multiple microseconds-long molecular-dynamics (MD) trajectories were generated usin

85 ts, the agreement of simulation results from molecular dynamics, Metropolis Monte Carlo, and kinetic

86 Supported by molecular dynamics modeling, we show that mildly selecti

87 al structures, using the Multiscale Reactive Molecular Dynamics (MS-RMD) methodology.

88 ay, we show that the density scaling law for molecular dynamics near the glass transition provides a

89 We call this method molecular dynamics phenotype prediction model.

90 hod also reproduces the experimental and the molecular dynamics product ratios within 15% for more th

91 Molecular dynamics provide atomic-level insight into the

92 Temperature profile and molecular dynamics reveal proton hopping at low activati

93 Molecular dynamics revealed that altered end-to-end bond

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

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

96 Molecular dynamics simulation and fluorescence resonance

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

98 Molecular dynamics simulation and normal mode analysis m

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

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

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

102 Molecular dynamics simulation indicates that, in the abs

103 Molecular dynamics simulation infers that facet-dependen

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

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

106 Molecular dynamics simulation results indicate high conf

107 Molecular dynamics simulation revealed that the R1060C m

108 Atomistic molecular dynamics simulation reveals short-range polar

109 Molecular dynamics simulation showed that indole alloste

110 Experiment and molecular dynamics simulation suggest that the stabiliza

111 Moreover, molecular dynamics simulation suggests that the central

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

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

114 Using molecular dynamics simulation, we demonstrate that the p

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

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

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

118 0.25 +/- 0.05) and those calculated from the molecular dynamics simulations (<E(FRET)(MD)> = 0.18 +/-

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

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

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

122 Steered molecular dynamics simulations allowed us to rationalize

123 Our molecular dynamics simulations also suggest that membran

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

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

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

127 We describe extensive molecular dynamics simulations and analysis on physiolog

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

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

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

131 Molecular dynamics simulations and studies in cells reve

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

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

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

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

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

137 Herein, molecular dynamics simulations based on a recently solve

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

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

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

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

142 Previous molecular dynamics simulations conducted by our group ha

143 Molecular dynamics simulations confirm the existence of

144 Here, we perform molecular dynamics simulations for Caulobacter crescentu

145 10-mus molecular dynamics simulations further correlated Omega-

146 Molecular dynamics simulations gave information on the g

147 Molecular dynamics simulations give an insight into the

148 Many molecular dynamics simulations have investigated phase s

149 Molecular modeling and molecular dynamics simulations identify models for these

150 Molecular dynamics simulations indicate different contac

151 Molecular dynamics simulations indicate that hardening i

152 Atomistic molecular dynamics simulations indicate this is because

153 Molecular dynamics simulations indicated that the onset

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

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

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

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

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

159 Molecular dynamics simulations of cone GAFab revealed di

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

161 Molecular dynamics simulations of DOM model compounds ca

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

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

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

165 Atomistic molecular dynamics simulations of P2 on model membrane s

166 Molecular dynamics simulations of post-powerstroke myosi

167 Molecular dynamics simulations of post-powerstroke myosi

168 Molecular dynamics simulations of such ions bearing intr

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

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

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

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

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

174 Molecular dynamics simulations of TREK1 in the presence

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

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

177 The results of molecular dynamics simulations performed on ganglioside-

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

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

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

181 Finally, molecular dynamics simulations provided a detailed struc

182 Molecular dynamics simulations provided structural expla

183 Extensive molecular dynamics simulations provided useful mechanist

184 Molecular dynamics simulations reinforce the experimenta

185 Molecular dynamics simulations reveal compensatory roles

186 Coarse-grained molecular dynamics simulations reveal that the transloco

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

188 Molecular dynamics simulations revealed that at low pH,

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

190 Molecular dynamics simulations revealed that the p.Arg29

191 Molecular dynamics simulations revealed that the x-ray s

192 Molecular dynamics simulations show a selective enrichme

193 Molecular dynamics simulations show that an understandin

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

195 Ab initio molecular dynamics simulations show these high conductiv

196 Molecular dynamics simulations showed that specific muta

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

198 Here, we use molecular dynamics simulations showing sequence differen

199 Atomistic molecular dynamics simulations starting from SAS-6 head

200 In turn, molecular dynamics simulations suggest altered VSD expos

201 Molecular dynamics simulations suggest that AimB binds M

202 Furthermore, molecular dynamics simulations suggest that lipids can f

203 Finally, molecular dynamics simulations suggest that modulation o

204 Molecular dynamics simulations suggest that the anionic

205 Molecular dynamics simulations suggested that SvBAHD05 i

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

226 Modelling and molecular dynamics simulations were fully consistent wit

227 Molecular dynamics simulations were performed with four

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

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

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

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

232 By combining molecular dynamics simulations with kinetic modeling, we

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

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

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

236 Homology modeling, molecular dynamics simulations, and lysosomal localizati

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

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

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

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

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

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

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

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

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

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

247 Molecular dynamics simulations, together with surface ma

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

266 temperature measurements were correlated to molecular dynamics simulations.

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

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

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

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

271 and theoretical predictions were made using molecular dynamics simulations.

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

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

274 c surface plasmon resonance measurements and molecular dynamics simulations.

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

276 uterium exchange mass spectrometry data with molecular dynamics simulations.

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

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

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

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

281 onents by energy landscape determination and molecular dynamics simulations.

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

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

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

285 These distributions were confirmed by molecular dynamics simulations.

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

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

288 Using steered molecular dynamics (SMD) simulations, we demonstrate tha

289 Molecular dynamics studies of the receptor have focused

290 combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamic

291 Through experimental and molecular dynamics studies, we demonstrated the role of

292 in a variety of applications that range from molecular dynamics to astrophysics.

293 trometry and nuclear magnetic resonance with molecular dynamics to evaluate the differential local st

294 We use ab initio non-adiabatic molecular dynamics to show that native point defects in

295 The use of WWF may reveal the changes in molecular dynamics underlying the higher water requireme

296 we have applied explicit solvent constant pH molecular dynamics using the multisite lambda-dynamics a

297 king simulations, pharmacophore modeling and molecular dynamics was applied and computational results

298 Unsteady molecular dynamics was used to study the pore formation

299 (THz) absorption spectroscopy and ab initio molecular dynamics, we have investigated the ambient wat

300 Using ab initio molecular dynamics, we identify the origin of the cataly