ライフサイエンスコーパス: coarse-grain

1 r molecular dynamics simulations, RACER (RnA CoarsE-gRained).

2 the dynamics, and both RNAs and proteins are coarse grained.

3 of network visualization, data ordering and coarse-graining.

4 for network visualization, data ordering and coarse-graining accomplished this goal.

5 A coarse-grained alumina could also reach a translucency l

6 coupled to yellow and consistent crumb, with coarse grain and well-perceivable sour taste and odor.

7 nal approaches-statistical mechanical model, coarse-grained and all-atom MD simulations-reveal that t

8 In both coarse-grained and all-atom molecular dynamics simulatio

9 combine molecular simulations based on both coarse-grained and atomistic models with coevolutionary

10 Here, we combined coarse-grained and atomistic simulations to model the ho

11 rate single-molecule force measurements with coarse-grained and atomistic simulations to resolve the

12 and electrical properties compared to their coarse-grained and nanograined counterparts.

13 based multiscale simulations where a dynamic coarse-graining and force-blending method is required.

14 time-dependent multidimensional data with a coarse-grained approach and map key dynamical features w

15 eld that are now underway, our physics-based coarse-grained approach to protein-structure prediction

16 Here, we use a multistage atomistic-coarse-grained approach, complemented by circular dichro

17 complementary roles that both atomistic and coarse-grained approaches play in such simulations.

18 tainment strategies are usually devised from coarse-grained assumptions about human mobility.

19 ious mathematical models of modal gating are coarse grained at the level of whole-channel states, lim

20 protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of tr

21 The framework consists of a coarse-grained but mechanistic description of host physi

22 mented landscapes rather than using averaged coarse-grained cells.

23 This approach uses the Martini coarse grain (CG) model to describe the receptors, lipid

24 Compared to coarse grained (CG) counterparts, swelling resistance of

25 (48 J/cm(2)) is almost comparable to that of coarse grained (CG) Cu: 55 J/cm(2).

26 In such cases, starting with coarse grained (CG) representations that were originally

27 Coarse-grain (CG) molecular dynamics simulations are emp

28 neous diffusivity of defect clusters in both coarse-grained (CG) and NP Ag.

29 By recourse to a coarse-grained (CG) model that captures the molecular st

30 Coarse-grained (CG) models in molecular dynamics (MD) ar

31 gnaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations

32 rosecond-scale explicit-solvent all-atom and coarse-grained (CG) molecular dynamics (MD) simulations.

33 These simulations use an explicit coarse-grained computational model that treats both the

34 ation of torsional and tensile loads using a coarse-grained computational model.

35 Here, we use coarse-grained computer simulations and the theory of as

36 vice for ab initio loop modeling combining a coarse-grained conformational search with a full-atom re

37 We hereby devise a new knowledge-based, coarse-grained contact potential, so-called ICOSA, by co

38 rs of magnitude higher than those in typical coarse-grained copper.

39 mics simulations with combined atomistic and coarse-grained description of NPs reveal the emergence o

40 Remarkably, a coarse-grained description of the system, based on the u

41 er demonstrates the capability of the "quasi-coarse-grained dynamics" (QCGD) simulation method to unr

42 Results presented here utilize coarse-grained elastic network modeling to extract the d

43 For this purpose, we utilize coarse-grained elastic network models.

44 easured DEER distributions, we constructed a coarse-grained elastic-network structural model of the c

45 olids and nonperturbative approach (by super-coarse-graining elasticity into internal bending modes)

46 ny-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively

47 Using a coarse-grained energy landscape model, we predict the st

48 ct on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots.

49 he second law of thermodynamics for bare and coarse grained entropy production and the flow of inform

50 greater room-temperature strength than their coarse-grained equivalents, in part owing to a large red

51 with computational approaches, marrying the coarse-grained experimental data with higher-resolution

52 We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanop

53 mulate model lipid bilayers with the MARTINI coarse-grained force field on length scales of tens of n

54 r membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids aroun

55 dress this need, we propose a novel reactive coarse-grained force field, as well as a publicly availa

56 rigid-body protein docking with the ATTRACT coarse-grained force field, as well as various kinds of

57 e dedicated equipment or limit themselves to coarse-grained force measurements on the micron scale.

58 n-specific signatures could be mapped to our coarse-grained framework to study self-assembly behavior

59 ural interpolation for the construction of a coarse-grained free energy landscape.

60 improved radiation tolerance comparing with coarse-grained, fully dense Au.

61 can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as

62 ph sampling protocol to construct and sample coarse-grained graph representations of RNAs from a give

63 fiber model, which couples fine-grained and coarse-grained HbS fiber models through a mesoscopic ada

64 Because of its large size, coarse graining helps to simplify and to aid in the unde

65 In this study, we used a combination of coarse graining, hierarchical natural move Monte Carlo a

66 We employed coarse-grained Langevin dynamics simulations to monitor

67 tial vegetation climate envelope models (for coarse-grained, large-scale predictions).

68 Here, we show that a coarse-grained lattice model like that of Chandler, when

69 ures of the clustered particle filtering are coarse-grained localization through the clustering of th

70 More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic

71 SpringSaLaD models biomolecules in a coarse-grained manner as a group of linked spherical sit

72 Here, we have extended the coarse-grain Martini force field to include RNA after ou

73 In this work, a combination of coarse-grained "Martini" and all-atom simulations are us

74 Here we construct and analyze a coarse-grained mathematical model of the fission yeast r

75 To this end, we performed coarse-grain MD simulations of the Photosystem II comple

76 We also performed Go-type coarse-grained MD of several structured and unstructured

77 Coarse-grained MD reveals that the lipids reorganize loc

78 Using a combination of all-atom and coarse-grained MD simulations and sequence covariation a

79 xplanation for the appropriately discretized/coarse-grained MD torsion angles data in a polypeptide i

80 r measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained resul

81 uniform tensile elongation characteristic of coarse-grained metals.

82 We have developed a coarse-grained method to simulate how individual transgl

83 We developed a coarse-grained method, PCalign, to quantitatively evalua

84 Efficient coarse-graining methods are required to reduce the intra

85 So far, exact and heuristic coarse-graining methods have been mostly restricted to t

86 first time an all-atom reconstruction from a coarse grained model has been performed in a relatively

87 esults were compared to both simulation of a coarse-grained model and experiment results.

88 We study Protein L folding using a coarse-grained model and molecular dynamics simulations.

89 The present coarse-grained model can provide a general way for explo

90 to deal with a complex system is to build a coarse-grained model capable of catching its main physic

91 Here, we have used a coarse-grained model describing the relation between obs

92 Molecular dynamics simulations using a coarse-grained model enables estimation of free-energy l

93 We use an accurate coarse-grained model for DNA and stochastic molecular dy

94 ic generalization of a previously introduced coarse-grained model for stabilization of proteins by su

95 Using a unique coarse-grained model for the power stroke of a single MV

96 nd Molecular Dynamics simulations to study a coarse-grained model of cement formation, and investigat

97 Using a coarse-grained model of DNA and lac repressor (LacI) in

98 We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately pr

99 Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influ

100 In this article, a coarse-grained model of pilus extension and attachment i

101 Here, we present a simple two-dimensional coarse-grained model of protein domain swapping in the c

102 xperiments, we performed simulations using a coarse-grained model of RNA to describe the response of

103 placement reaction with a recently developed coarse-grained model of RNA.

104 e perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elu

105 A computationally efficient coarse-grained model of the erythrocyte membrane reveals

106 ere we extend our previous study that used a coarse-grained model of the F1-ATPase to generate a stru

107 We use molecular simulations by creating a coarse-grained model of the MT-kinesin complex, which re

108 roximately 8 degrees ) using a residue-level coarse-grained model of the ribosome.

109 The coarse-grained model of the SNARE complex is calibrated

110 Combining these two parts, the coarse-grained model of the SNARE complex with membrane

111 /membrane deformation with an apparently new coarse-grained model of the SNARE complex.

112 ssipative particle dynamics simulations of a coarse-grained model of the system revealed its tendency

113 The coarse-grained model previously developed in our lab has

114 In this work, we present a generic coarse-grained model that captures the formation of self

115 erformed molecular dynamics simulations on a coarse-grained model that describes virus assembly on a

116 Here, we introduce a coarse-grained model that enables simulation of networks

117 timescales of fusion, we developed a highly coarse-grained model that retains key biophysical SNARE

118 Here, we report a newly developed coarse-grained model to predict the structure of SSB-ssD

119 We present a new coarse-grained model to realistically simulate the bindi

120 We use a coarse-grained model to represent proteins with varying

121 The coarse-grained model we consider is that of Ginzburg-Lan

122 We use our coarse-grained model with a set of secondary structural

123 rded as the simplest and most representative coarse-grained model, has been widely adopted to analyze

124 Using simulations of the TOPRNA coarse-grained model, we show that increased topological

125 We have applied a structure-based coarse-grained model, with an explicit Debye-Huckel char

126 lustering process using a recently developed coarse-grained model.

127 sely matching the level of resolution of the coarse-grained model.

128 Experimental and coarse-grain modeling results reveal that systematic Mn

129 stant pH molecular dynamics simulations with coarse-grained modeling and yields new, atomic-level, in

130 attering with X-rays and neutrons coupled to coarse-grained modeling reveal that the intrinsically di

131 We performed systematic coarse-grained modeling using an elastic network model a

132 ons of these assemblies include all-atom and coarse-grained modeling, but modeling their conformation

133 ere we demonstrate, through a combination of coarse-grained modeling, isothermal calorimetry, and str

134 Here we show atomistic, coarse-grained modelling combined with advanced simulati

135 Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling

136 uantum mechanics and larger length scales of coarse-grain models.

137 tion results have previously been limited to coarse-grained models (at varying levels of resolution).

138 affinity of calcium (Ca(2+)) by integrating coarse-grained models and all-atomistic simulations with

139 folded proteins using atomistic simulations, coarse-grained models and analytic theory.

140 The binding mechanism suggests that coarse-grained models are appropriate to study the motio

141 Coarse-grained models are compared with 3D cryo-electron

142 hesis, and most conventional structure-based coarse-grained models do not allow for nonnative structu

143 In this review we provide an overview of coarse-grained models focusing on their design, includin

144 e explore how APs achieve this by developing coarse-grained models for clathrin and AP2, employing a

145 For this reason, coarse-grained models have been used successfully.

146 n length for a spherical droplet; the use of coarse-grained models in the calculation of the interfac

147 Inevitably, such coarse-grained models introduce a set of phenomenologica

148 dy and analysis, construction of atomic from coarse-grained models is required.

149 ch that instead constructs phenomenological, coarse-grained models of network dynamics that automatic

150 te calculations have only been performed for coarse-grained models of water.

151 Coarse-grained models represent attractive approaches to

152 led description is given for applications of coarse-grained models suitable for efficient combination

153 However, most existing coarse-grained models use extremely simple potentials to

154 mputations--how can we efficiently construct coarse-grained models whose description of the dynamics

155 imulation approach that blends atomistic and coarse-grained models.

156 uctures given by all-atom models and that by coarse-grained models.

157 t few lowest frequency modes than with other coarse-grained models.

158 ng arguments and interpreted in terms of two coarse-grained models.

159 edure is general and can be adapted to other coarse-grained models.

160 Coarse grain molecular dynamics simulations revealed spo

161 mines its overall stiffness, we introduced a coarse-grain molecular dynamics model of the axon membra

162 Coarse-grain molecular dynamics simulations are a key to

163 We performed comparative atomistic and coarse-grain molecular-dynamics simulations of the LEL i

164 Thermodynamic analysis and coarse-grained molecular dynamic simulations indicate th

165 lop a two-step multiscale framework based on coarse-grained molecular dynamics (CGMD) and dissipative

166 ar magnetic resonance (NMR) spectroscopy and coarse-grained molecular dynamics (MD) simulations, we f

167 dvanced computational approach that combines Coarse-Grained molecular dynamics and well-tempered Meta

168 By using a multiscale coarse-grained molecular dynamics approach, we show that

169 We present OpenRBC, a coarse-grained molecular dynamics code, which is capable

170 his complex stochastic system using advanced coarse-grained molecular dynamics modeling of tubulin-tu

171 t a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master

172 Using a novel, validated coarse-grained molecular dynamics simulation approach, h

173 We test this framework using coarse-grained molecular dynamics simulations and find i

174 Previously, we used coarse-grained molecular dynamics simulations and free e

175 experimental studies are also supported with coarse-grained molecular dynamics simulations and molecu

176 Coarse-grained molecular dynamics simulations are applie

177 mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing

178 correlated with the density predictions from coarse-grained molecular dynamics simulations in the cen

179 Consistent with this possibility, extensive coarse-grained molecular dynamics simulations of a BR tr

180 tor oligomerization we carried out extensive coarse-grained molecular dynamics simulations of crystal

181 iscuss progress in the area of atomistic and coarse-grained molecular dynamics simulations of selecte

182 We present coarse-grained molecular dynamics simulations of the eps

183 Coarse-grained molecular dynamics simulations of the str

184 Coarse-grained molecular dynamics simulations reveal a n

185 We do this using coarse-grained molecular dynamics simulations specifical

186 Here, we use high-throughput coarse-grained molecular dynamics simulations to charact

187 t into these systems, the present study used coarse-grained molecular dynamics simulations to describ

188 We used coarse-grained molecular dynamics simulations to examine

189 In this study, we use coarse-grained molecular dynamics simulations to explore

190 Here, we use atomistic and coarse-grained molecular dynamics simulations to investi

191 Supporting coarse-grained molecular dynamics simulations uncover th

192 Using coarse-grained molecular dynamics simulations we have ex

193 Both coarse-grained molecular dynamics simulations, and X-ray

194 A combination of coarse-grained molecular dynamics simulations, Laurdan m

195 By using coarse-grained molecular dynamics simulations, we show t

196 These results were successfully modeled by coarse-grained molecular dynamics simulations, which als

197 We present coarse-grained molecular dynamics simulations, which rev

198 dent site-specific (1)H-(15)N HSQC data with coarse-grained molecular dynamics simulations.

199 lar structure of a BAR-domain scaffold using coarse-grained molecular dynamics simulations.

200 terized from nearly 200 mus of residue-based coarse-grained molecular dynamics simulations.

201 Umbrella sampling and coarse-grained molecular dynamics were employed to calcu

202 In this work, using coarse-grained molecular dynamics, the transmembrane dom

203 hate (PIP2) -containing lipid bilayer, using coarse-grained molecular dynamics.

204 n in human Hepatitis B virus in vivo using a coarse-grained molecular model that captures the essenti

205 on, we develop a particle model-resembling a coarse-grained molecular model-constructed to match the

206 reaction, and demonstrates the potential of coarse-grained molecular simulation approaches for inves

207 Here we employ coarse-grained molecular simulations to show that indivi

208 er experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C

209 Coarse-grained molecular simulations, which mimic glass

210 dated by experimental NMR measurements, with coarse-grained Monte Carlo simulations of 24-nucleosome

211 Coarse-grained Monte-Carlo simulations of the system are

212 The late addition of coarse-grained NaCl (crystal size: 0.4-1.4 mm) to pizza

213 -screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motio

214 lly combining the Morone-Makse algorithm and coarse graining of the network in which we regard a comm

215 It has been recently shown that the coarse-graining of the structures of polypeptide chains

216 r beds typically have an "armoured" layer of coarse grains on the surface, which acts to protect fine

217 l of protein representation from all-atom to coarse-grained opens up new possibilities for studying p

218 Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to

219 In this work, we develop a coarse-grained particle-based computational model for ca

220 a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated ov

221 Although the coarse-grained patterning resembles that created by scal

222 These responses can be interpreted using a coarse-grained physical description of the cortex in ter

223 are related through computations on a model coarse-grained polymer melt, with and without nanopartic

224 present the proposed formalism to construct coarse-grained potential models for three examples: an i

225 Water is described with the mW coarse-grained potential, where hydrogen-bonds are model

226 ICOSA also outperforms a set of widely used coarse-grained potentials and is comparable to all-atom,

227 ating the sequence-derived and residue-level coarse-grained potentials with the interface structure p

228 Using molecular dynamics simulations of coarse-grained predictive energy landscape models for th

229 to improve model elaboration, refinement and coarse graining procedures to better understand the rele

230 We use coarse grained protein conformational search, efficient

231 etric binding energies for each state of the coarse-grained protein corresponding to the symmetry of

232 bly of single nucleosomes using a predictive coarse-grained protein DNA model with transferable force

233 A predictive coarse-grained protein force field [associative memory,

234 Using a predictive coarse-grained protein force field, we compute and compa

235 f homologous protein sequences and develop a coarse-grained protein model specifically tailored to co

236 ng whether MS-based footprinting can provide coarse-grained protein structure by following structural

237 approach, expanding the recently established coarse-grained proteome allocation models from steady-st

238 evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, t

239 ory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which al

240 th different force-fields (both all-atom and coarse grained representations).

241 Coarse-grained representations of the input network enab

242 tion that make use of either atomic-level or coarse-grained representations.

243 es of molecular dynamics (MD) simulations at coarse-grained resolution for both the wild-type (WT) an

244 el geometry and stream-flow records from 186 coarse-grained rivers across the United States.

245 ures, we have developed an open software for coarse-grained RNA folding simulations, guided by human

246 We introduce a coarse-grained RNA model for molecular dynamics simulati

247 We develop a coarse-grained simulation approach for predicting equili

248 Coarse-grained simulation approach is applied to provide

249 e integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted e

250 Unlike most coarse-grained simulation approaches, the higher-level o

251 ationally demanding than fully atomistic and coarse-grained simulation methodologies; however, it has

252 We present a coarse-grained simulation model that is capable of simul

253 Using a coarse-grained simulation model, we can reproduce the kn

254 Using a coarse-grained simulation model, we rationalized that th

255 We use a coarse-grained simulation that takes into account the di

256 -molecule force-spectroscopy experiments and coarse-grained simulation.

257 with phosphatidylethanolamine using multiple coarse-grain simulations.

258 mbine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical ca

259 A folding, and demonstrates the potential of coarse-grained simulations as a tool for rationally tuni

260 lecular modeling using atomic resolution and coarse-grained simulations corroborates our experimental

261 and instead support a model put forward from coarse-grained simulations indicating that binding is me

262 Coarse-grained simulations of a wide range of junction t

263 We present coarse-grained simulations of capsid assembly under vari

264 certainty by demonstrating the capability of coarse-grained simulations of membrane protein insertion

265 Using coarse-grained simulations of peptide self-assembly, we

266 using a combination of rigidity analysis and coarse-grained simulations of protein motion.

267 The coarse-grained simulations quantitatively reproduce the

268 Combining theory and coarse-grained simulations shows that the DNA sequence a

269 We use coarse-grained simulations to investigate the Sec-facili

270 ational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis

271 se atomistic molecular-dynamics simulations, coarse-grained simulations, and a statistical-mechanical

272 e ribosome's mechanism can be extracted from coarse-grained simulations, including the ratchet motion

273 Similar dynamical structures are observed in coarse-grained simulations, suggesting that defect-order

274 junction structure evaluated by all-atom and coarse-grained simulations.

275 we fused site-specific NMR information with coarse-grained simulations.

276 ential for the NTD in AMPA-type iGluRs using coarse-grained simulations.

277 plectonemes, and study its properties using coarse-grained simulations.

278 (ACO) and long-range order (LRO), as well as coarse-grained simulations; the stability arises from a

279 We carried out coarse-grained spatial stochastic binding simulations fo

280 Our coarse-grained structural model thus suggests that the h

281 als to represent the interactions within the coarse-grained structures and as a result, the dynamics

282 p between the quality of the dynamics of the coarse-grained structures given by all-atom models and t

283 d as a result, the dynamics obtained for the coarse-grained structures may not always be fully realis

284 els whose description of the dynamics of the coarse-grained structures remains as accurate as that gi

285 We coarse grain the resulting kinetic model at two levels:

286 Although coarse-grained, the trade-offs that the model embodies a

287 Complementing our previous coarse-grained theoretical results, our simulations give

288 In this study, we use a well-established coarse-grained three-dimensional model of DNA and seven

289 irregularity of the sign time series of its coarse-grained time series at different time scales.

290 in difficulties by applying a gradient-based coarse graining to RNA-ligand systems and solving the pr

291 le microstructural damage in single-crystal, coarse-grained, ultrafine-grained and nanograined metals

292 Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to pre

293 ein-folding trajectories, generated with the coarse-grained united-residue force field, for the B dom

294 linked to the equilibrium statistics of the coarse-grain variables.

295 eled as a monomer with restraints applied to coarse-grained variables enforced to keep it in a filame

296 The network can be taught in situ using a coarse-grain variety of the delta rule algorithm to perf

297 The continuum equations can be viewed as a coarse-grained version of previously developed discrete

298 ved membranes; and 2) the self-assembly of a coarse-grained virus capsid protein model.

299 rute-force molecular dynamics simulations of coarse-grained water on top of different surfaces of a m

300 nical and atomistic descriptions to derive a coarse-grained yet chemically specific representation th