ライフサイエンスコーパス: molecular mechanics

1 treated quantum mechanically, and 35 287, by molecular mechanics).

2 ill provide insight into their functions and molecular mechanics.

3 e size (R) using a proposed hybrid continuum-molecular mechanics.

4 e-grained molecular dynamics simulations and molecular mechanics.

5 identified using a rapid algorithm based on molecular mechanics.

6 ts, because they create flows that alter the molecular mechanics.

7 Molecular mechanics (Amber) and semiempirical (AM1) calc

8 ime-dependent UV-vis spectroscopy, HPLC, and molecular mechanics analyses revealed an atypical therma

9 in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics sim

10 ering method along with optimizations at the molecular mechanics and density functional M06-2X levels

11 Molecular mechanics and density functional theory (M06-2

12 Molecular mechanics and dynamics calculations were also

13 iments and theoretically by a combination of molecular mechanics and electronic structure calculation

14 wledge-based scoring functions, and MM-GBSA (molecular mechanics and generalized Born surface area),

15 Molecular mechanics and molecular dynamics calculations

16 Homology modeling with molecular mechanics and molecular dynamics simulations e

17 Molecular mechanics and molecular dynamics studies of th

18 We present basic concepts of molecular mechanics and polymer physics relevant to the

19 Here, through a combination of molecular mechanics and quantum mechanics calculations,

20 We have used a combination of molecular mechanics and semiempirical calculations toget

21 eved using in vacuo energy minimization with molecular mechanics and statistically derived continuous

22 on (XRD) and computational modeling based on molecular mechanics and two-dimensional XRD simulations

23 ct protein structures typically include both molecular-mechanics and knowledge-based terms.

24 solvent molecular dynamics, implicit solvent molecular mechanics, and quantum mechanics with a self-c

25 m force field is a suitable tool for various molecular mechanics applications on large macromolecular

26 We have used a molecular mechanics approach to perform tensile tests on

27 tide bond using a combined quantum mechanics/molecular mechanics approach together with adaptive umbr

28 ructure and using a hybrid quantum mechanics/molecular mechanics approach, we investigate the pathway

29 te this reaction step by a quantum-mechanics/molecular-mechanics approach in combination with molecul

30 mechanisms that cannot be captured under the molecular mechanics approximations, and which therefore

31 ular dynamics simulations using ligand-field molecular mechanics are performed to elucidate, for the

32 Thermodynamic values were reproduced using molecular mechanics augmented by ab initio calculations

33 ve site encouraged study of the reaction via molecular mechanics-based free energy minimization.

34 rotocol consists of hybrid quantum mechanics-molecular mechanics-based high temperature Langevin mole

35 -chain rotamer sampling in the interface and molecular-mechanics-based energy calculations.

36 /hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's.

37 Based on molecular mechanics calculation, the formation of the di

38 oach involves the following steps: (i) using molecular mechanics calculations (with, e.g., MacroModel

39 Here, we reconcile these results using molecular mechanics calculations and an implicit membran

40 Molecular modeling, molecular mechanics calculations and molecular dynamics

41 Quantum mechanics/molecular mechanics calculations are employed to assign

42 Molecular mechanics calculations are employed to explore

43 ecular dynamics and hybrid quantum mechanics/molecular mechanics calculations at the mPW1N/6-311+G(2d

44 e developed a coarse-grained force field for molecular mechanics calculations based on the virtual in

45 (b) Molecular mechanics calculations demonstrate that the st

46 ical force field-based and quantum mechanics/molecular mechanics calculations for modeling the nucleo

47 Quantum and molecular mechanics calculations for the Diels-Alder rea

48 Combined quantum mechanics and molecular mechanics calculations further indicate that i

49 NMR studies and molecular mechanics calculations indicated that the impr

50 r dynamics simulations and quantum mechanics/molecular mechanics calculations indicated that, for the

51 equirements from ab initio quantum mechanics/molecular mechanics calculations of activation free ener

52 We performed quantum mechanics/molecular mechanics calculations on the N-terminal domai

53 nes in the R series and also on the basis of molecular mechanics calculations performed on the entire

54 Molecular mechanics calculations revealed that this reco

55 Molecular mechanics calculations reveals a correlation b

56 Side chain conformational analysis by molecular mechanics calculations showed that the side ch

57 Molecular mechanics calculations suggested 1a as the mos

58 g, molecular dynamics, and excitonic quantum/molecular mechanics calculations to examine and rational

59 nctional theory and hybrid quantum mechanics/molecular mechanics calculations to investigate this rea

60 ve survey of the potential energy surface by molecular mechanics calculations using AMBER has provide

61 By quantum mechanics/molecular mechanics calculations we show that the critic

62 sotropic displacement parameters (ADPs), and molecular mechanics calculations were used to analyze th

63 ectroscopy, X-ray crystallography, classical molecular mechanics calculations, and normal-coordinate

64 We perform quantum mechanics/molecular mechanics calculations, considering the glycin

65 Molecular mechanics calculations, corroborated by experi

66 d-flow, rapid-quench flow, quantum/mechanics molecular mechanics calculations, crystallography, and d

67 died by X-ray crystal structure analysis and molecular mechanics calculations, including docking of t

68 computational methods, including docking and molecular mechanics calculations, we have been able to c

69 In the present work, using quantum mechanics/molecular mechanics calculations, we investigate the ele

70 cs simulations, and mixed quantum mechanical/molecular mechanics calculations, yielding a comprehensi

71 are supported by mixed quantum mechanics and molecular mechanics calculations.

72 r dynamics simulations and quantum mechanics/molecular mechanics calculations.

73 ce of O(6)-alkylguanine, as determined using molecular mechanics calculations.

74 mics simulations and ONIOM quantum mechanics/molecular mechanics calculations.

75 stances for these complexes match those from molecular mechanics calculations.

76 astereomeric aldehydes were predicted, using molecular mechanics calculations.

77 lar dynamics ab initio and quantum mechanics/molecular mechanics calculations.

78 nzene in the solid state were computed using molecular mechanics calculations.

79 led by performing a conformational search by molecular mechanics calculations.

80 ecules have been computed with ab initio and molecular mechanics calculations.

81 y and X-ray crystallography, corroborated by molecular mechanics calculations.

82 (log K = 5.7 +/- 0.1) that was predicted by molecular mechanics calculations.

83 fine-shifted 1H NMR spectrum of CoAbeta, and molecular mechanics calculations.

84 edge-based potential functions, and all-atom molecular mechanics calculations.

85 mulated, based on combined quantum-classical molecular mechanics calculations.

86 ndent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as

87 bonate membrane, which itself was bound to a molecular mechanics chamber.

88 tions of inhibitor-kinase complexes with the molecular mechanics code GROMACS.

89 solution were elucidated by combined NMR and molecular mechanics computational techniques, showing th

90 ependent DFT, and combined quantum mechanics/molecular mechanics computations.

91 tion of distance constraint information into molecular mechanics conformational searches can be used

92 ty functional theory based quantum mechanics-molecular mechanics dynamical modeling.

93 Boltzmann-weighted probabilities from these molecular mechanics energies compare well with database-

94 , we describe the first tests of the ROSETTA molecular mechanics energy function in the context of ol

95 These features are based on molecular mechanics energy functions, stereochemical eff

96 arious continuum components are derived from molecular-mechanics energy calculations using the CHARMM

97 Design provides a new avenue for testing molecular-mechanics energy functions, and future improve

98 ssively methyl-substituted systems by use of molecular mechanics estimates of differences in strain b

99 re was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanis

100 While the molecular-mechanics field has standardized on a few pote

101 We therefore explored the use of molecular mechanics for constructing rotamer libraries f

102 the best of the other methods, including the molecular mechanics force field AMBER99.

103 tential multipole moment (EPMM) or classical molecular mechanics force field single-point partial cha

104 Here, we examine the extent to which the molecular mechanics force field used in such simulations

105 dge-based potential, after optimization in a molecular mechanics force field.

106 next-generation method for the validation of molecular mechanics force fields and chemical shift pred

107 development of the most recent generation of molecular mechanics force fields promises an increasingl

108 Molecular mechanics force fields that explicitly account

109 to test the ability of a variety of popular molecular mechanics force fields to maintain the native

110 highly relevant for the parameterization of molecular mechanics force fields which form the basis of

111 The MutaBind method uses molecular mechanics force fields, statistical potentials

112 classical as well as mixed quantum mechanics molecular mechanics force fields, we uncover a possible

113 Using a molecular-mechanics force field, we predict high-affinit

114 It is well-known that standard molecular-mechanics force fields used in most such calcu

115 ions when we simulate protein evolution with molecular-mechanics force fields.

116 e (WT) ecDHFR using hybrid quantum mechanics-molecular mechanics free energy simulations with the Met

117 It is based on variation of the molecular mechanics Generalized Born (MMGB) method, scal

118 dynamics simulations and binding free energy molecular mechanics-generalized born surface area (MM-GB

119 One such is afforded by molecular mechanics-generalized Born surface area (MM-GB

120 omputation of interaction energies using the Molecular Mechanics-Generalized Born Surface Area (MM-GB

121 Further, molecular mechanics-generalized Born surface area calcul

122 ng free-energy changes, calculated using the molecular mechanics-generalized Born surface area techni

123 A molecular mechanics-generalized Born/surface area analys

124 rmed using a similarity filter, docking, and molecular mechanics-generalized Born/surface area postpr

125 fts obtained in single point calculations on molecular mechanics geometries without computationally e

126 lly inexpensive single-point calculations on molecular mechanics geometries without time-consuming ab

127 ecular dynamics and hybrid quantum mechanics/molecular mechanics have been used to investigate the me

128 The effects of these mutations on myosin's molecular mechanics have not been determined.

129 Quantum mechanics/molecular mechanics hybrid molecular modeling revealed t

130 We describe a quantum mechanics/molecular mechanics investigation of the guanidinoacetat

131 In contrast, empirical ligand-field molecular mechanics (LFMM) captures the d-electron effec

132 rofluidic prototype validates the design for molecular mechanics measurements.

133 and laser trap assays are commonly used for molecular mechanics measurements.

134 sition state, we performed quantum mechanics/molecular mechanics metadynamics simulations of the glyc

135 d demonstrate, by means of quantum mechanics/molecular mechanics metadynamics simulations, that it is

136 the results from a hybrid quantum mechanics/molecular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber)

137 ADI by using an ab initio quantum mechanics/molecular mechanics method.

138 wn N-layer integrated molecular orbital plus molecular mechanics) method, we report a comprehensive t

139 nstrate that computational quantum mechanics/molecular mechanics methods can provide reasonable value

140 Cr(N=C-t-Bu(2))(4) using density functional/molecular mechanics methods confirmed the qualitative an

141 theoretical framework to combine quantum and molecular mechanics methods, and compute the effect of m

142 ctional theory, and hybrid quantum mechanics/molecular mechanics methods.

143 m mechanics, combined quantum mechanics, and molecular mechanics methods.

144 cular mechanics package) (quantum mechanical:molecular mechanics) methods to calculate FTIR differenc

145 is determined using X-ray diffraction (XRD), molecular mechanics (MM) and molecular dynamics (MD) sim

146 with imprinted cavities were simulated with molecular mechanics (MM) and molecular dynamics (MD).

147 of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular

148 tional studies of nucleic acids have applied Molecular Mechanics (MM) approaches using simple pairwis

149 ds that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify

150 We first evaluated the accuracy of molecular mechanics (MM) for the prediction of rotamer p

151 density functional theory (DFT) coupled with molecular mechanics (MM) methods.

152 d using virtual mutagenesis and optimized by molecular mechanics (MM) minimization.

153 oyed QM (density functional theory and MP2), molecular mechanics (MM), and molecular dynamics (MD) me

154 on step, a computational analysis, including molecular mechanics (MMFF94) and semiempirical AM1 geome

155 An elastic DNA molecular mechanics model is used to compare DNA structu

156 A molecular mechanics model of the complex formed between

157 We introduce a quantum mechanics/molecular mechanics model of the oxygen-evolving complex

158 Molecular mechanics modeling was used to help design a c

159 bation theory to construct quantum-mechanics/molecular-mechanics models of Az48W(*) and ReAz108W(*) c

160 Coarse-grain molecular-mechanics models provide a detailed picture of

161 bsorption measurements and quantum mechanics/molecular mechanics molecular dynamics simulations allow

162 called GlmU through hybrid quantum mechanics-molecular mechanics molecular dynamics simulations and f

163 n the context of ab initio quantum mechanics/molecular mechanics molecular dynamics, we examined cert

164 loying ab initio QM/MM-MD (Quantum Mechanics/Molecular Mechanics-Molecular Dynamics) simulations with

165 Overall, our results shed light on the molecular mechanics of hair-cell sensory transduction an

166 The interactions among these enzymes and the molecular mechanics of how separation occurs without lys

167 ntitative systems platform that utilizes the molecular mechanics of ion transport, metabolism, and si

168 Our findings provide new insights into the molecular mechanics of mammalian miRNA-mediated gene sil

169 Little is known about the molecular mechanics of the late events of translation in

170 isms of nociception and thermosensation, the molecular mechanics of these ion channels are still larg

171 step toward a detailed understanding of the molecular mechanics of this important signal transductio

172 Our dissection of the molecular mechanics of vertebrate tooth replacement coup

173 or a theoretical analysis (quantum mechanics/molecular mechanics) of the mechanism of chemistry witho

174 l methods (ligand docking, quantum mechanics/molecular mechanics optimization, and molecular dynamic

175 own N-layered integrated molecular Orbital + Molecular mechanics package) (quantum mechanical:molecul

176 Using the Q2MM method, new molecular mechanics parameters were developed to perform

177 tive stabilities of the interfaces using the molecular mechanics Poisson-Boltzmann solvent accessible

178 Molecular mechanics Poisson-Boltzmann surface area (MM-P

179 Free energy decomposition by molecular mechanics Poisson-Boltzmann surface area (MM-P

180 Thermodynamic analyses using molecular mechanics Poisson-Boltzmann surface area (MM-P

181 We present results using the molecular mechanics Poisson-Boltzmann surface area (MM-P

182 The recently described molecular mechanics Poisson-Boltzmann surface area (MM-P

183 Herein we report an application of the molecular mechanics Poisson-Boltzmann surface area (MM/P

184 o investigate the sensitivity of the popular molecular mechanics Poisson-Boltzmann surface area (MMPB

185 rmation, we employed two additional methods: Molecular Mechanics Poisson-Boltzmann Surface Area (MMPB

186 intermediate has been characterized using a molecular mechanics Poisson-Boltzmann surface area appro

187 Computational alanine scanning using the molecular mechanics Poisson-Boltzmann surface area metho

188 molecular dynamic simulations combined with Molecular Mechanics-Poisson Boltzmann Surface Area calcu

189 mation rigid docking, solvation docking, and molecular mechanics-Poisson-Boltzmann/surface area (MM-P

190 ilic and mesophilic TBPs by using a combined molecular mechanics/Poisson-Boltzmann approach.

191 ute binding free energies were calculated by molecular mechanics/Poisson-Boltzmann surface area (MM/

192 extensive molecular dynamics simulations and molecular mechanics/Poisson-Boltzmann surface area (MM/P

193 igands into a sigma(1) 3D homology model via molecular mechanics/Poisson-Boltzmann surface area calcu

194 evelopment of a CHARMM (Chemistry at Harvard Molecular Mechanics) polarizable force field for simulat

195 Here we show that a standard molecular-mechanics potential energy function without an

196 A molecular-mechanics potential is used to reconstruct the

197 and and the 10 primary contact residues, the molecular-mechanics potential is used to redesign a ribo

198 ion method and show that, of the traditional molecular mechanics potentials tested, only one showed a

199 The application of unmodified molecular-mechanics potentials to protein design links t

200 e fct-FePt as suggested by quantum mechanics-molecular mechanics (QM-MM) simulations.

201 Furthermore, a quantum mechanics/molecular mechanics (QM/MM) analysis suggests that the f

202 We performed a detailed quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD)

203 ite 8-oxoguanine using the quantum mechanics/molecular mechanics (QM/MM) approach, both from a chemis

204 Via a quantum mechanics/molecular mechanics (QM/MM) approach, the calculated fre

205 By using a quantum mechanics/molecular mechanics (QM/MM) approach, we propose a mecha

206 investigated by means of a quantum mechanics/molecular mechanics (QM/MM) approach.

207 e embedded in DNA using a quantum mechanical/molecular mechanics (QM/MM) approach.

208 ults utilizing a combined quantum mechanical molecular mechanics (QM/MM) approach.

209 rocessing unit (GPU)-based quantum mechanics/molecular mechanics (QM/MM) approaches.

210 Quantum mechanics/molecular mechanics (QM/MM) calculations combined with f

211 MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have been carri

212 MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have been carri

213 actions were modeled using mixed quantum and molecular mechanics (QM/MM) calculations in the context

214 ctional theory (DFT)-based quantum mechanics/molecular mechanics (QM/MM) calculations of the crystals

215 mics (MD) simulations and quantum-mechanical/molecular mechanics (QM/MM) calculations of the fatty ac

216 unctional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations on the full enz

217 Quantum mechanics and molecular mechanics (QM/MM) calculations tested the prop

218 ) simulations and combined quantum mechanics/molecular mechanics (QM/MM) calculations to elucidate th

219 expensive and specialized quantum mechanics/molecular mechanics (QM/MM) calculations to provide a qu

220 ntegration, and high-level quantum mechanics/molecular mechanics (QM/MM) calculations to study the po

221 variation of selectivity, mixed quantum and molecular mechanics (QM/MM) calculations were carried ou

222 Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a mo

223 Based on quantum mechanics/molecular mechanics (QM/MM) calculations, the free energ

224 e complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations.

225 mics simulations and ONIOM quantum mechanics/molecular mechanics (QM/MM) calculations.

226 MD) simulations and mixed quantum mechanical/molecular mechanics (QM/MM) calculations.

227 pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations.

228 DNA dodecamer by means of quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations.

229 In this work, mixed quantum and molecular mechanics (QM/MM) combined with Monte Carlo si

230 aracterized at the uniform quantum mechanics/molecular mechanics (QM/MM) computational level using de

231 lecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and pu

232 D) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate th

233 se (RNase) H1 using hybrid quantum-mechanics/molecular mechanics (QM/MM) free energy calculations.

234 Combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations revea

235 ording to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, in conjuncti

236 Quantum mechanics/molecular mechanics (QM/MM) maturation of an immunoglobu

237 carried out using a hybrid quantum mechanics/molecular mechanics (QM/MM) method.

238 Combining quantum and molecular mechanics (QM/MM) methods and protein structur

239 Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in thi

240 x geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods, (3) conformational

241 hods in concert with mixed quantum mechanics/molecular mechanics (QM/MM) methods, the hydroxylation o

242 ion modelling using hybrid quantum mechanics/molecular mechanics (QM/MM) methods.

243 R pK(a) determination with quantum mechanics/molecular mechanics (QM/MM) modeling to study engineered

244 application of hybrid quantum mechanics and molecular mechanics (QM/MM) models is an important appro

245 quantum mechanics (QM) and quantum mechanics/molecular mechanics (QM/MM) models of the UDG active sit

246 evelopment of the combined quantum mechanics/molecular mechanics (QM/MM) models.

247 eaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the

248 d approach based on hybrid quantum mechanics/molecular mechanics (QM/MM) simulation.

249 demonstrated by the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of light-harvest

250 cs calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a varie

251 onance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies

252 We use mixed quantum mechanics/molecular mechanics (QM/MM) techniques in a constrained

253 Using linear-scaling quantum mechanics/molecular mechanics (QM/MM) techniques with more than 50

254 gstrom resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction

255 y correlation behavior and quantum mechanics/molecular mechanics (QM/MM) trajectories point to a domi

256 We have used combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular

257 ions and hybrid approaches combining QM with molecular mechanics (QM/MM).

258 r the first time by hybrid quantum mechanics/molecular mechanics (QM/MM).

259 edded PSII with high-level quantum-mechanics/molecular-mechanics (QM/MM) calculations of individual a

260 n n-layered integrated molecular orbital and molecular mechanics(quantum mechanics:quantum mechanics'

261 Molecular mechanics results suggest that in the smallest

262 calculated with a finite cluster model using molecular mechanics revealed a symmetric but nonsinusoid

263 ectroscopy and restrained molecular dynamics/molecular mechanics (rMD/MM) calculations using 179 NOE

264 Molecular mechanics simulations elucidates the multiplic

265 es and non-adiabatic mixed quantum mechanics/molecular mechanics simulations in the phthalocyanine-fu

266 on is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effect

267 Our results are pertinent to quantum and molecular mechanics simulations of ligands bound to GPCR

268 Restrained molecular mechanics simulations on an existing x-ray str

269 Molecular mechanics simulations suggest that these C-sha

270 Molecular mechanics simulations support a commensurate s

271 , we carried out extensive quantum mechanics/molecular mechanics simulations to calculate stepwise he

272 e density functional theory calculations and molecular mechanics simulations to estimate the strength

273 We use quantum mechanics/molecular mechanics simulations to study the cleavage of

274 al models by combining quantum mechanics and molecular mechanics simulations with time-resolved Fouri

275 n of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyse

276 Ion mobility measurements, combined with molecular mechanics simulations, are used to study enant

277 Using quantum mechanics/molecular mechanics simulations, we delineate a reaction

278 In hybrid quantum mechanics/molecular mechanics simulations, we observe that reducti

279 d dynamic first-principles quantum mechanics/molecular mechanics simulations.

280 e-activating protein using quantum mechanics/molecular mechanics simulations.

281 intermolecular interactions with ligands via molecular mechanics simulations.

282 e phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations.

283 ts are predicted by hybrid quantum mechanics/molecular mechanics simulations.

284 g software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for

285 g software, HostDesigner, is interfaced with molecular mechanics software, GMMX, providing a tool for

286 In this work we present a quantum mechanics/molecular mechanics study into the mechanism of sulfoxid

287 We report a hybrid density functional theory-molecular mechanics study of the mechanism of the additi

288 e the basis for a detailed quantum mechanics/molecular mechanics study of the path for the complete t

289 Combining accurate mixed quantum mechanics/molecular mechanics techniques and protein structure pre

290 tent-charge density functional tight binding/molecular mechanics, the bond lengths in the concerted m

291 By quantum mechanics/molecular mechanics, the computed free energy barrier of

292 ecular dynamics and hybrid quantum mechanics/molecular mechanics to analyze sequence context-dependen

293 We used molecular mechanics to illustrate conformations found by

294 ent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted

295 n for proteins that we call the virtual atom molecular mechanics (VAMM) force field.

296 sitions with our coarse-grained virtual atom molecular mechanics (VAMM) potential function.

297 onal theory and multiscale quantum mechanics/molecular mechanics, we report C-terminal cleavage react

298 mics simulation and hybrid quantum mechanics/molecular mechanics, we show that ferric peroxo addition

299 Homology modeling and molecular mechanics were used to build a structural mode

300 e apply a high-throughput formulation of the molecular mechanics with Poisson-Boltzmann surface area