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-grained molecular dynamics simulations and molecular mechanics.

4 identified using a rapid algorithm based on molecular mechanics.

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

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

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

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

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

10 Molecular mechanics and dynamics calculations were also

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

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

13 Molecular mechanics and molecular dynamics calculations

14 ynthetase mutant enzymes were obtained using molecular mechanics and molecular dynamics simulation te

15 Homology modeling with molecular mechanics and molecular dynamics simulations e

16 Molecular mechanics and molecular dynamics studies of th

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

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

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

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

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

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

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

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

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

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

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

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

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

30 on, and their chiral structures optimized by molecular mechanics are discussed.

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

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

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

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

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

39 Molecular modeling, molecular mechanics calculations and molecular dynamics

40 Quantum mechanics/molecular mechanics calculations are employed to assign

41 Molecular mechanics calculations are employed to explore

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

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

44 (b) Molecular mechanics calculations demonstrate that the st

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

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

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

48 combination of density functional theory and molecular mechanics calculations has been used to study

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 Seventy-five quantum mechanics/molecular mechanics calculations of the energies of reac

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

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

55 Molecular mechanics calculations revealed that this reco

56 Molecular mechanics calculations reveals a correlation b

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

58 Molecular mechanics calculations suggested 1a as the mos

59 and (S)-7 have been used in combination with molecular mechanics calculations to examine the prevaili

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

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

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

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

64 formations were established by ab initio and molecular mechanics calculations, 1D and 2D (1)H NMR spe

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

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

67 Molecular mechanics calculations, corroborated by experi

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

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

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

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

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

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

74 astereomeric aldehydes were predicted, using molecular mechanics calculations.

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

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

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

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

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

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

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

82 ppage of the trityl groups was obtained from molecular mechanics calculations.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

102 ge, a detailed all-atom protein model with a molecular mechanics force field is not necessary to reac

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 An adapted MM3 molecular mechanics force field, specifically parametriz

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

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

108 In contrast, molecular mechanics force fields commonly used for biomo

109 It is precisely such effects that molecular mechanics force fields have not captured.

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

111 Molecular mechanics force fields that explicitly account

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

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

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

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

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

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

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

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

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

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

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

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

124 A molecular mechanics-generalized Born/surface area analys

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

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

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

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

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

130 are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with h

131 Quantum mechanics/molecular mechanics hybrid molecular modeling revealed t

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

133 a DNA oligomer, derived from NMR restrained molecular mechanics, is presented.

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

135 rofluidic prototype validates the design for molecular mechanics measurements.

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

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

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

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

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

141 udied by means of a hybrid quantum mechanics/molecular mechanics method.

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

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

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

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

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

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

148 experiments were interpreted with the aid of molecular mechanics (MM) and density functional theory (

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

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

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

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

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

154 The calculations utilized a molecular mechanics (MM) force field with physical inter

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

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

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

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

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

160 A molecular mechanics model of the complex formed between

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

162 Molecular mechanics modeling was used to help design a c

163 combination with distance calculations using molecular mechanics modeling, the experimental results f

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

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

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

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

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

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

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

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

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

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

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

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

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

177 ronment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field te

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

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

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

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

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

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

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

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

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

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

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

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 The binding affinities calculated by molecular mechanics/Poisson-Boltzmann surface accessibil

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

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

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

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

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

197 A molecular-mechanics potential is used to reconstruct the

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

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

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

201 e field results and hybrid quantum mechanics/molecular mechanics predictions.

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

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

204 Combining accurate mixed quantum mechanics/molecular mechanics (QM/MM) and protein structure predic

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 proton-transfer process, a quantum mechanics/molecular mechanics (QM/MM) model is constructed from th

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

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

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

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

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

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

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

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

257 Molecular mechanics results suggest that in the smallest

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

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

260 emical shift predictions were performed with molecular mechanics, semiempirical, ab initio, and densi

261 our simulations and in the reported all-atom molecular mechanics simulation studies may be mainly due

262 Molecular mechanics simulations elucidates the multiplic

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

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

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

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

267 Molecular mechanics simulations suggest that these C-sha

268 Molecular mechanics simulations support a commensurate s

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

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

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

272 rgies of all dimer conformations in all-atom molecular mechanics simulations with explicit water.

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

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

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

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

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

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

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

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

281 intermolecular interactions with ligands via molecular mechanics simulations.

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

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

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

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

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

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

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

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

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

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

292 We used molecular mechanics to illustrate conformations found by

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

294 state of our knowledge and ignorance of the molecular mechanics underlying eukaryotic translation.

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