ライフサイエンスコーパス: force field

1 interactions (a term neglected in classical force fields).

2 preceeding a second movement performed in a force field.

3 ween the anisotropic friction and the active force field.

4 r-Stokes equations for reacting species in a force field.

5 tion models produced using a modified CHARMM force field.

6 s solution exploiting a newly developed TiO2 force field.

7 al and the environment by means of the AMBER force field.

8 ements while only one arm was subjected to a force field.

9 after optimization in a molecular mechanics force field.

10 simulation under the control of the original force field.

11 apparently reflect approximations of the DNA force field.

12 (AWSEM), a predictive coarse-grained protein force field.

13 ly induced via the external application of a force field.

14 id membrane environment based on the Martini force field.

15 ns so that this structure could deform under force field.

16 le geometric measure, inness, that maps this force field.

17 day 1), day 2 involved adaptation to a novel force field.

18 stic simulations with the AMOEBA polarizable force field.

19 -grained protein DNA model with transferable force fields.

20 that are often poorly described by standard force fields.

21 cles has been implemented using a variety of force fields.

22 gning protein folding simulation methods and force fields.

23 imulation with the CHARMM36 and Amber ff12SB force fields.

24 would have some key advantages over standard force fields.

25 een limited due to the absence of applicable force fields.

26 tools can stimulate improvement of existing force fields.

27 represented on a simpler level by empirical force fields.

28 solvent model and different well-established force fields.

29 op refolding simulations with four different force fields.

30 ions is the highly approximate nature of the force fields.

31 phatidylcholine lipids using CHARMM and OPLS force fields.

32 alculations currently relying exclusively on force fields.

33 M) approaches using simple pairwise-additive force fields.

34 e protein evolution with molecular-mechanics force fields.

35 nd is an essential ingredient in polarizable force fields.

36 evaluate the performance of newly developed force fields.

37 nerated by MD simulations with two different force fields.

38 g the functional forms of publicly available force fields.

39 ee text] (exchange), in contrast to standard force fields.

40 FTB) method with a molecular mechanical (MM) force field, a QM/MM model was built to describe the rea

41 ry cortex (S1) applied concurrently with the force field abolished the ability to update subsequent m

42 This suggests that force field adaptation is associated with an increase in

43 Force field adaptation, a type of cerebellum-dependent m

44 matics (visuomotor adaptation) and dynamics (force-field adaptation).

45 strate that for both object manipulation and force-field adaptation, contrary to previous models, mem

46 dipole moments calculated using polarizable force fields also revealed that water molecules remainin

47 molecular dynamics combined with the PRIME20 force field and a newly built inhibitor model are perfor

48 mpact on the development of advanced protein force field and folding simulation methods.

49 cular dynamics simulations using a realistic force field and including quantum effects support this i

50 s of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded A

51 ferent correlation patterns observed between force field and structural quality for the models with t

52 ible with respect to the choice of molecular force field and the number of discretization levels in t

53 found that MD simulations with the AMBER-03w force field and the TIP4P/2005s water model are able to

54 It utilizes a chemically accurate force field and thermodynamic sampling to improve the re

55 od for the validation of molecular mechanics force fields and chemical shift prediction algorithms.

56 for protein mechanisms obtained by different force fields and correct for a wide range of stationary

57 etermined using quantum mechanics (QM)-based force fields and grand canonical Monte Carlo (GCMC) simu

58 the benefits of shorter protocols and latest force fields and maintaining the crystal waters for accu

59 PELDOR experiments correctly rank DNA force fields and resolve subtle differences in the confo

60 gy calculations have benefited from improved force fields and sampling algorithms, as well as the adv

61 ults suggest that the use and calibration of force fields and solvent models for precise estimation o

62 s of minimization and MD steps, 10 different force fields and three different water models.

63 ted here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA

64 formed with three different state-of-the-art force fields and validated by experimental NMR measureme

65 e conformational energies computed with CABS force-field and residue states is approximated using a c

66 work we have parametrized accurate classical force-fields and used these to compute the conformationa

67 wise or counter-clockwise velocity-dependent force field, and one session in a null field.

68 ined force field of ClayFF, constant-valence force field, and SPC water model.

69 s for evaluating improved molecular dynamics force fields, and also will enable further development o

70 op accurate force fields, including reactive force fields, and chemically realistic surface models, t

71 g of chemical bonding, in the development of force fields, and in the development of chemically reali

72 ul assessment and evaluation of new methods, force fields, and modeling innovations on well-character

73 e rugged energy landscapes using polarizable force fields, and the hydration number profiles of these

74 quantification of high-resolution continuous force fields, and the simultaneous capability of this me

75 rmed a locomotor adaptation task (perturbing force field applied to the ankle during swing using a ro

76 statistical associating fluid theory (SAFT) force field are used to interrogate the incipient solidi

77 ale poorly to large systems, while classical force fields are cheap and scalable, but lack transferab

78 s that advanced polarizable atomic multipole force fields are efficient enough to repack the entire h

79 Two distance-transform based "force" fields are used: one for "pressure", which is the

80 Last generation of force-fields are raising expectations on the quality of

81 ons, carried out using multiple nucleic acid force fields, are used to demonstrate that partial base-

82 ntal free energies, even when using the same force field as previous computational studies that were

83 MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution

84 We interpreted the Thy1 force fields as representations of spinal motor modules.

85 tein docking with the ATTRACT coarse-grained force field, as well as various kinds of protein flexibi

86 As intended, force-field assistance directly strengthened the relatio

87 We used the force-field assisted refinement method, molecular dynami

88 rm would demonstrate greater adaptability to force fields associated with the opposite arm's movement

89 A predictive coarse-grained protein force field [associative memory, water-mediated, structu

90 ware, biomolecular simulations with advanced force fields at biologically relevant timescales are bec

91 ons of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER.

92 tempering, metadynamics, and one of the best force-fields available.

93 nformation and an energy landscape optimized force field (AWSEM), we predict atomic-scale structures

94 DA occasionally sampled the pathway space of force field-based DIMS MD.

95 nteractions or condensed phase properties by force field-based methods require a precise description

96 ansferases were investigated using empirical force field-based simulations.

97 l and experimental findings by using a fully force-field-based and GPU-accelerated approach, which al

98 ransitions in MD simulations and reduces the force-field bias.

99 ly suffer from incomplete sampling or from a force-field bias.

100 inverted-hexagonal phase, and with different force-fields (both all-atom and coarse grained represent

101 hose obtained using last generation of AMBER force-fields (BSC1 and BSC0OL15) show predictive power i

102 On day 3, patients readapted to the force field but all groups now received neutral feedback

103 emporal and spatial profile of the generated force fields but also on the mechanical properties of th

104 Force field calculations revealed that the barrier to ro

105 On the basis of X-ray structures and force field calculations, the overall potency of this se

106 These results illustrate how the CamTube force field can be used to explore efficiently the unive

107 The coupling of these two force fields can "push" a "rolling ball" quickly along t

108 Consequently, classical force fields can be used to study the wetting of F/H-ter

109 icted contacts as restraints but without any force fields can yield correct folds (i.e., TMscore>0.6)

110 tional analysis revealed only one particular force field capable of retaining the transient helical m

111 Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36.

112 ted using umbrella sampling with a classical force field ("classical" model).

113 on membrane and provide passive (no external force fields), continuous filtration, thus eliminating t

114 lecular dynamics simulations using atomistic force fields could provide such insight, but are not fea

115 volunteers performed reaching movements in a force-field created by a robotic device.

116 t with our previous study, adaptation to the force field decreased gradually as the movement directio

117 of such approaches is the inaccuracy of the force field design, which cannot accurately describe the

118 molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physica

119 Residue (UNRES) physics-based coarse-grained force field, developed in our laboratory for the predict

120 nt and generalization of MD water models for force-field development, macromolecular crystallography,

121 relative to the null session, regardless of force field direction, in the straight-ahead dimension (

122 served for , indicating that revision of the force-field employed by GLYCAM is probably needed.

123 The approach (called "xGen") augments a force field energy calculation with an electron density

124 ion methods minimize hand-designed molecular force field energy functions that are often not well cor

125 tion theory to consistently treat systematic force-field error and statistical errors in simulation a

126 gn allows a huge enhancement of the magnetic force field experienced by paramagnetic molecular specie

127 hanism is hampered by the fact that existing force fields fail to capture the correct balance of TMAO

128 g steps: (1) conformation generation using a force field (FF)-based method, (2) filtering the FF gene

129 of currently used chemically specific lipid force fields (FF) such as the CHARMM, AMBER, GROMOS, OPL

130 arting from disagreeing simulations with the force fields ff96, ff99, ff99sbnmr-ildn, CHARMM27, and O

131 In a significant departure from conventional force-field fitting, we use a multilevel evolutionary st

132 The Martini model, a coarse-grained force field for biomolecular simulations, has found a br

133 lecular simulations that utilize an accurate force field for calcium ions with scaled charges effecti

134 rge model for water and an accurate flexible force field for CO(2).

135 ther nonbonded energy functions, a dedicated force field for conformational and nonbonded protein int

136 We present parmbsc1, a force field for DNA atomistic simulation, which has been

137 y (DFM) to quantitatively map the tip-sample force field for naphthalene tetracarboxylic diimide mole

138 Here, we show that a universally applicable force field for phosphorus can be created by machine lea

139 asis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates

140 SiCDC, and develop a novel first-principles force field for the simulation of adsorption and transpo

141 We developed the RexPoN force field for water based entirely on quantum mechanic

142 contribute to protein stability and thus in force fields for biomolecular modeling.

143 sing a composite physics and knowledge-based force fields for efficient protein structure refinement.

144 We also identified the most appropriate force fields for MD simulations of this IDP.

145 the power of accurate and flexible ML-driven force fields for next-generation materials modelling.

146 Most previous force fields for sphingomyelins were developed before th

147 rded to be among the most accurate classical force fields for this substance.

148 rated with the coarse-grained united-residue force field, for the B domain of staphylococcal protein

149 The force-field generated by a near-field optical trap is an

150 ps with respect to chain length despite both force fields generating different conformational ensembl

151 proaches based on mechanical actuation using force-field gradients have emerged as complementary tech

152 The C36 CHARMM lipid force field has been extended to include sphingolipids,

153 Whereas the quality of classical MD force fields has improved significantly in recent years,

154 A new generation of force-fields has been developed to better represent the

155 99chi_YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between structural fea

156 ch we show outperforms the additive CHARMM36 force field in both ion retention and maintenance of the

157 ial involving a combination of the INTERFACE force field in conjunction with ReaxFF and including Cou

158 ecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over 500 ns

159 rent atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the

160 as well as future directions, of polarizable force fields in biomolecular simulations.

161 bilities of molecular dynamics and classical force fields in describing spontaneous binding events an

162 es opportunities to further develop accurate force fields, including reactive force fields, and chemi

163 lected for unfolding as the magnitude of the force field increases.

164 d by unpredictable mechanical perturbations (force field) independent of their on-line corrections.

165 based on the incorporation of the 'CamTube' force field into the Gromacs molecular dynamics package.

166 The polarizable force field is based on a minimal set of fitting paramet

167 tamer isomerization barriers in the all-atom force field is found to further speed up refinement.

168 Our study demonstrates that a force field is not necessary, cryo-EM data alone is suff

169 The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and sim

170 f calculating the optical potential from the force-field is shown to be inaccurate when the trapping

171 eraction potentials are added to the CamTube force field, it is possible to fold a protein into a top

172 electronic structure via the wavefunction at force-field-like efficiency and captures quantum mechani

173 -end elimination with the polarizable AMOEBA force field lowered Rfree by 2.8-26.7% and improved mean

174 o relocate solutions against the centrifugal force field, making them newly accessible for downstream

175 zed energetics for biomolecular applications force field, many-body optimization theory, and graphica

176 es compared to the traditional physics-based force field methods.

177 ns than are those obtained from conventional force field methods.

178 provide initial coordinates for conventional force field methods.

179 vious predictions from a five-site empirical force-field model.

180 A, our study highlights basic limitations of force field modeling of nucleic acids.

181 problem, we used the MEDYAN mechano-chemical force field, modeling several micron-long actin bundles

182 calculations, and for the parametrization of force-field models used in fields ranging from crystallo

183 he molecular topology is based on the CHARMM force field, new complex sugar moieties can be generated

184 interactions were addressed by the combined force field of ClayFF, constant-valence force field, and

185 -protein interactions suggests the curvature force field of the membrane comes into play.

186 nd manipulate non-equilibrium structures and force fields of up to millimetre length scales(1-3).

187 pid bilayers with the MARTINI coarse-grained force field on length scales of tens of nanometers and t

188 the influence from water models and protein force fields on calculated profiles are insignificant up

189 We use the TIP4P/ice force field, one of the best existing molecular models o

190 licit solvent using two different simulation force fields (OPLS-AA/L and AMBER ff99SB-ILDN).

191 Fourth, two force fields, OPLS-AA and CHARMM22* have unique features

192 ional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated

193 Biomolecular force fields optimized for globular proteins fail to pro

194 lly without intervention through an external force field or a patterned track.

195 lecular dynamics simulations based on either force fields or density functional theory are used to de

196 face for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the forma

197 andbook is a public database and archive for force field parameters of small and drug-like molecules.

198 radual interpolation between the two sets of force field parameters that are representative of the no

199 this limitation that entails modification of force field parameters to reduce a few pairwise non-bond

200 g role in the development and testing of the force field parameters.

201 Here we present force-field parameters for one of the most common pairs

202 ater model, combined with three biomolecular force-field parameters for the protein part, significant

203 Recently, we have developed empirical force-field parameters to model lantibiotics.

204 o tackle the so-called rare events, improved force-field parameters, and the concomitant increasing a

205 dite humic acid, together with corresponding force-field parameters, available at the Vienna Soil Org

206 are particularly sensitive to the choice of force-field parameters, especially those defining the wa

207 r, voltages, electrolyte concentrations, and force-field parameters.

208 We describe the latest developments in Drude force field parametrization and application, primarily i

209 nce of MD simulations with the newly updated force-fields Parmbsc0epsilonzetaOLI and CHARMM36 was tes

210 lowing the introduction of a visuomotor or a force field perturbation, or the sudden removal of such

211 a task in which mixtures of error-clamp and force-field perturbation trials were used to deconstruct

212 mouse model to study forelimb adaptation to force field perturbations.

213 to velocity-dependent and position-dependent force-field perturbations (vFFs and pFFs) at the earlies

214 In contrast, force-field perturbations directly weakened the relation

215 ping based on the Protein-Ligand Informatics force field (PLIff).

216 r introduces the protein-ligand informatics "force field", PLIff, which begins to address these key c

217 eled by Newtonian dynamics of a conservative force field plus two asymmetrical dissipative terms.

218 First, all force fields predict that Abeta adopts unfolded structur

219 We find that the 12 force fields produce a wide range of predictions.

220 dynamics simulations carried out with modern force fields provide an accurate description of folding

221 ts derivatives rather than ff94 or polarized force fields provided the most accurate scoring and rank

222 ynamics simulations, performed with reactive force fields purposely built and extensively tested agai

223 using the Drude oscillator-based polarizable force field, quantum chemical calculations, and ONIOM mu

224 Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the

225 Parallel Simulator (LAMMPS) with a reactive force-field (ReaxFF).

226 Here, we compared performance of force fields recommended for intrinsically disordered pr

227 rated to be robust vis-a-vis a change in the force-field, reconciles the seemingly contradictory expe

228 have to be reconsidered and revised and that force field refinements are necessary for reliable simul

229 Evidently, the force field revisions to parm99 improve the modeling of

230 ry (DFT) with the semiempirical relativistic force field (RFF) method of Kutateladze and Mukhina (KM)

231 w that simulations using a sufficiently good force-field sample conformations that are valid but have

232 Using a novel hybrid empirical force field scoring function, CAT accurately ranks the d

233 r weight of vision vs. proprioception in the force field session relative to the null session, regard

234 ment (EPMM) or classical molecular mechanics force field single-point partial charges with Coulomb fo

235 Despite the progress made in force fields, small molecule parameterization remains an

236 The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain

237 Among Amber force fields tested, ff14SB and its derivatives rather t

238 With further improvements of the UNRES force field that are now underway, our physics-based coa

239 is significantly enhanced using an empirical force field that explicitly includes the treatment of el

240 ture of the study is the use of an atomistic force field that has been parametrised against experimen

241 ions in the current implicit solvent protein force field that must be sufficiently addressed for reli

242 of solutions, we have developed an optimized force field that reproduces experimental Kirkwood-Buff i

243 s inform the construction of system-specific force fields that describe each partner individually.

244 ht limitations of simulations with classical force fields that do not explicitly account for charge t

245 Molecular mechanics force fields that explicitly account for induced polariz

246 Participants were repeatedly exposed to a force-field that either assisted or perturbed the normal

247 is work, a predictive coarse-grained protein force field, the associative memory water-mediated struc

248 he presence of the entire nucleosome for all force fields, the secondary structure of the histone tai

249 Together with an efficient force field, these contacts allow us to determine struct

250 icit membrane potential and reoptimizing the force field to account for the differing nature of the i

251 relies on atomistic models and a polarizable force field to describe a material system and its dielec

252 y involved in the described processes with a force field to include environmental effects.

253 e, we have extended the coarse-grain Martini force field to include RNA after our recent extension to

254 These results indicate the polarizable force field to more accurately model peptide-folding coo

255 -based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Com

256 he complexity of the problem, using physical force field to predict the mutation-induced binding free

257 rget proteins with a recently improved UNRES force field to provide better reproductions of the local

258 vantage of xMDFF, which applies an optimized force field to realign molecular models during phasing b

259 e performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal s

260 ons also revealed some limitations in the CG force field to study protein assembly in solution, which

261 of the chip with respect to the centrifugal force field to time the passage of multiple components r

262 be modified to improve applicability of the force fields to both ordered and disordered proteins.

263 n computational power and molecular dynamics force fields to develop and test a realistically complex

264 cal principles and state-of-the-art all-atom force fields to predict both nucleosome occupancy along

265 k, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30

266 protein design methods rely on physics-based force fields to search for low free-energy states follow

267 his work we explore the ability of different force-fields to predict the structure of two new B-DNA d

268 following: (1) impaired adaptation to a new force field under TMS parietal perturbation; (2) defecti

269 reliability, improvements to the potentials/force fields underlying these tools are needed to avoid

270 free in solution and limitations in the DNA force-fields underpinning the simulations.

271 Boltzmann distribution corresponding to the force field used in the simulations.

272 ed tails but show a strong dependence on the force field used.

273 well-known that standard molecular-mechanics force fields used in most such calculations have a limit

274 ing free-energy landscapes correspond to the force fields used in the simulations.

275 cy of these models is limited by that of the force fields used to generate the underlying molecular d

276 s simulations performed, irrespective of the force-field used.

277 all-atom detail with a physically realistic force field using a standard computing cluster.

278 omponent and the solenoidal component of the force-field using Helmholtz-Hodge decomposition, it was

279 ; the net simulation time using Amber ff14SB force field was 61 mus.

280 simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfoldin

281 Using a predictive coarse-grained protein force field, we compute and compare the free energy land

282 Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of

283 namics simulations combined with the PRIME20 force field, we find that the Hu-, BV-, and SHaPrP(120-1

284 ecular dynamics simulations and transferable force fields, we designed a series of symmetric triblock

285 Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of an Escheric

286 of an interference experiment where opposing force fields were associated with two separate visual mo

287 We found that Thy1 force fields were more complex and diverse in structure

288 mic; additional simulations in which the two force fields were swapped suggest that these differences

289 er's predictions is a coarse-grained protein force field which has its roots in neural network ideas

290 r dynamics simulations based on the CHARMM36 force field, which could achieve only modest accord with

291 We applied the Drude polarizable force field, which we show outperforms the additive CHAR

292 ncated Abeta10-40 peptide produced with five force fields, which combine four protein parameterizatio

293 nformed by quantum-mechanically parametrized force fields, which identify the mechanisms underlying i

294 So parameterizing CG force fields, which is both tedious and time-consuming,

295 coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexp

296 on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most

297 Furthermore, when healthy subjects move in a force field with unpredictable dynamics, they have activ

298 o not address directly the critical need for force fields with polarizability and multipoles, and con

299 Two of the force fields yield compact nonnative states with misplac

300 Additionally, both force fields yield very similar thermodynamic scaling re