ライフサイエンスコーパス: free energy

1 and amplitude of the order parameter in the free energy.

2 es reside at the global minimum of the Gibbs free energy.

3 or spatial variations in the diffusivity and free energy.

4 e same orientation to be a global minimum of free energy.

5 on approximately doubles the agonist-binding free energy.

6 ased on the minimization of Landau-de Gennes free energy.

7 or producing scalable and sustainable carbon-free energy.

8 ible for these drastically different binding free energies.

9 ion with molecular dynamics simulation of ET free energies.

10 Free energy analysis shows that the structural orders wi

11 urther allows us to predict absolute binding free energies and analyze reaction kinetics using Markov

12 ship between the experimental conformational free energies and computed molecular orbital energies wa

13 , affecting temperature contributions to the free energy and impacting reaction rate and equilibrium

14 l biomass (theoretical yield) based on Gibbs free energy and microbially available electrons.

15 We have carried out free energy and molecular dynamics studies to determine

16 entropic penalty, resulting in total higher free energy and reduced ligand affinity.

17 neighbor parameters were derived for use in free energy and secondary structure prediction software.

18 and mineral contribute to values of binding free energy and that changes in pH and ionic strength pr

19 ay out the relation between relative binding free energy and the overall reversible covalent binding

20 hose of cyclic 2-azadienes, and the reaction free energies are 17-20 kcal mol(-1) more endergonic.

21 material removal; this calculated change of free energy associated with sliding revealed that there

22 hermodynamic calculation of electric current free energy at various microstructure configurations.

23 y if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free

24 a nanoscale channel requires overcoming the free energy barrier associated with confinement.

25 brium, this framework demonstrates a lowered free energy barrier at the solid-solution interface in t

26 At a concentration of 40 muM, the clear free energy barrier between the pre-fibrillar tetramer f

27 as-phase NHC-CO2 bond distance and the Gibbs free energy barrier for decarboxylation is demonstrated.

28 ns for the SpnF-catalyzed reaction predict a free energy barrier of 22 kcal/mol for the concerted Die

29 The calculated free energy barrier of the reactions revealed that anili

30 active and active states separated by a high free energy barrier resulting in switch-like activation.

31 responds to a 6-kcal/mol higher dissociation free energy barrier.

32 ic and entropic components in the rotational free energy barrier.

33 ), dominant at short times, and a pronounced free-energy barrier at the transition from the epidermis

34 ke kinetics, suggestive of the crossing of a free-energy barrier between two phases.

35 Free-energy barrier heights calculated for critical step

36 TM electrical field considerably lowers the free-energy barrier in the direction of F-form to I-form

37 n of a molecular trajectory during which the free-energy barrier is crossed.

38 Reduction potentials and free energy barriers calculated at the CPCM-B3LYP/6-31+G

39 Calculated free energy barriers for 1 reasonably agree with experim

40 RCCSD(T)/cc-pVDZ//UBLYP/cc-pVDZ free energy barriers for 1,4-H shifts at 298 K are consi

41 ecular simulations characterizing the rates, free energy barriers, and mechanism of water evaporation

42 portant nonclassical effects: the nucleation free-energy barriers are reduced eightfold compared with

43 organic conversions but has to overcome high free-energy barriers in water.

44 resent the broadest validation of a rigorous free energy-based approach applied to protein stability

45 Here, we incorporate a mechanochemical free-energy-based approach to elucidate how the two-way

46 While the N-H bond dissociation free energy (BDFE) of 5H(2-) (230 +/- 4 kJ mol(-1)) and

47 ate-determining step has a bond dissociation free energy (BDFE) of approximately 32 kcal mol(-1).

48 We find that the differences in free energy between the individual complexes in bulk wat

49 pose that Rgg2Sp* mutations invoke shifts in free-energy bias to favor the active state of the protei

50 operate efficiently, we investigate how this free energy budget can be allocated to maximize flux.

51 g a certain number of ATP, providing a fixed free energy budget.

52 erforming molecular dynamics simulations and free energy calculation of Activin-Like Kinase 2 (ALK2),

53 g, docking followed by manual filtering, and free energy calculations (FEP).

54 Absolute binding free energy calculations based on alchemical pathways pr

55 We evaluated the performance of free energy calculations based on molecular dynamics for

56 Binding free energy calculations based on molecular simulations

57 e in a large-scale validation, that rigorous free energy calculations can be used to predict changes

58 In recent years, atomistic free energy calculations have proven to be a valid tool

59 Free energy calculations identify residues that metastab

60 Free energy calculations indicate that the high rate is

61 Free energy calculations indicated that K-Ras dimerizati

62 s for hydrogen evolution, according to Gibbs free energy calculations of H-adsorption on Mo2B4.

63 n analysis of parameter usage during folding free energy calculations of stochastic samples of second

64 ve either building QSAR models or performing free energy calculations of the permeation event.

65 Free energy calculations provide the barriers to evapora

66 The binding free energy calculations show that the Glu361 and His447

67 Here we use rare-event sampling and free energy calculations with the mW water model to show

68 According to our simulations and free energy calculations, the Gly1629Glu mutation causes

69 roscopy, molecular dynamics simulations, and free energy calculations.

70 for different proteins can be estimated via free energy calculations.

71 These findings highlight the importance of free-energy calculations in drug design, confirming that

72 From these free-energy calculations, we determined the kinetics and

73 molecular dynamics simulations, and binding free-energy calculations.

74 showed negative entropy, enthalpy and Gibbs free energy change at 25 degrees C.

75 Br(-)](+*) was due to a less favorable Gibbs free energy change for electron transfer that resulted i

76 The Gibbs free energy change for reactions of inactivation of sele

77 For all agonists and sites, the total free energy change in each pathway was the same, confirm

78 rotein-protein interfaces, where the binding free-energy change (DeltaDeltaG) is counted as the logar

79 ield to predict the mutation-induced binding free-energy change remains challenging.

80 This highlights the role of modest free energy changes in the folding of pre-integration fo

81 s, mutation induced globular protein folding free energy changes, and mutation induced membrane prote

82 stood as reflecting additive and independent free energy changes, without assuming any specific inter

83 nd mutation induced membrane protein folding free energy changes.

84 uted to a markedly small difference in Gibbs free energy compared to the known similar class of mater

85 Free energy components include van der Waals, hydrogen b

86 ormula: see text]4 [Formula: see text]s) and free energy computations for different chemical states o

87 The interplay between interface- and volume-free energies controls both the structure and compositio

88 amics simulations were used to calculate the free energy cost of inverting the side-chain stereochemi

89 ains predict this value, indicating that the free energy cost of knot formation is of entropic origin

90 ergy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediat

91 re we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured

92 concentrations and do not take into account free energy costs that may be associated with structural

93 end on the magnitudes of side-chain transfer free energies (DeltaDeltaGsc(o)).

94 FE) of 5H(2-) (230 +/- 4 kJ mol(-1)) and the free energy DeltaG degrees PCET for the reaction with TE

95 disproportionates with a tremendous loss of free energy, DeltaG(o) = -2.6 eV.

96 reduction over a range of negative reaction free energies, DeltarG, that were obtained by systematic

97 ns of 5 mus duration, as well as by computed free energy difference between the active and desensitiz

98 e-Zn(2+) coordination geometry, reflecting a free energy difference of only 0.5 kcal/mol.

99 average lifetime of the MCA is 36 ms and the free energy difference to the TSA-like form is 8.5 kJ/mo

100 fied the impact of the R551A mutation on the free-energy difference between the active and autoinhibi

101 tension, which is well tailored to match the free-energy difference between the inactive (bent-closed

102 ng the breaking and rebinding to determine a free-energy difference, DeltaG, of 6 kcal.mol(-1) betwee

103 g of global interfacial tension coupled with free energy dissipation has been used to give an energet

104 his compensates the increment of interfacial free energy during breaking up and enables the processin

105 The highest lifetime, lowest free-energy ensemble identified consisted of native conf

106 DFT-derived formation free energies for alkoxides with different framework att

107 The activation free energies for the Diels-Alder reactions of cyclic 1-

108 8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions.

109 The predicted relative binding free energies for three ligands binding to the progester

110 We obtained the partitioning free energy for all 20 amino acids at the lipid-facing i

111 terparts, while maintaining nearly identical free energy for DNA hybridization compared with free DNA

112 hese clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the ef

113 Association constant and Gibbs free energy for the interaction of anti-OTA/Protein-A/PS

114 Association constant and Gibbs free energy for the interaction of Glass/ZnO-NRs/Protein

115 ea correlated directly with the partitioning free energy for the lipid-facing residue and inversely w

116 lecular dynamics, which show that the excess free energy for the three equilibrium structures correla

117 estimate of the absolute ligand/DNA binding free energy ([Formula: see text] = -10.3 +/- 0.5 kcal/mo

118 based string method to solve for the minimum free-energy gating pathways of the proton-activated bact

119 ner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to wate

120 analogy between the fitness function and the free energy in statistical mechanics, allowing us to use

121 endent substep, and find that the associated free energy input supports the mechanism involving concu

122 Electric current free energy is dependent on the microstructure configura

123 ich approximately 1.0 kcal/mol of scrunching free energy is generated per translocation step of RNA s

124 93 A) and the sequence-specific variation of free energy is in excellent agreement with experimentall

125 Modeling of the conformational free energy landscape (FEL) of a thioglycoside strongly

126 umvent kinetic traps in their conformational free energy landscape and fold efficiently to the native

127 tailed representations of the conformational free energy landscape and the complex folding mechanism

128 on hairpin substrates with an optimized flat free energy landscape containing all binding motifs allo

129 Our free energy landscape depicts a low barrier for the perm

130 tadynamics simulations of the conformational free energy landscape for the cyclopropyl inhibitors sho

131 4 isoform, reflecting how S672R remodels the free energy landscape for the modulation of HCN4 by cAMP

132 Dynamic force spectroscopy can probe the free energy landscape of interacting bonds, but interpre

133 ect of SAM and magnesium ions on the folding free energy landscape of the SAM-I riboswitch.

134 m ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch.

135 he barrier creates a transition state in the free energy landscape that slows fibril formation and cr

136 lica exchange with solute tempering, and the free energy landscape was explored by metadynamics.

137 mputing trajectories that are shown upon the free energy landscape.

138 ion for the construction of a coarse-grained free energy landscape.

139 th and the protein as a random walker in the free energy landscape.

140 h the prefusion trimer and rationalizing the free-energy landscape of this conformational machine.

141 ents between such states enabled the folding free-energy landscape to be deduced.

142 state arising from the combination of a flat free-energy landscape, a fragmented local structure, and

143 peptide detachment was defined solely by the free-energy landscape.

144 (d[AG3(T2AG3)3]), computing also the binding free-energy landscape.

145 tein force field, we compute and compare the free energy landscapes and relative stabilities of amylo

146 Free energy landscapes can be generated for both cPCA an

147 Quantum mechanical calculations of the free energy landscapes reveal how the neutral inhibitors

148 ture variations are highlighted on projected free energy landscapes.

149 and energy model (AWSEM) to construct their free energy landscapes.

150 a coarse-grained model enables estimation of free-energy landscapes for the interactions of 12 differ

151 material, a discrepancy occurs in the Gibbs free energy leading to a difference in oxidation peak po

152 The free energy maps of AMPA and kainate receptor ATD dimers

153 ng mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), whic

154 to 2017, each demonstrating that alchemical free energy methods can assist rational drug design proj

155 n this review, we describe the principles of free energy methods used for the calculation of protein-

156 pirical approaches to rigorous physics-based free energy methods.

157 ransition-path sampling and high-performance free-energy methods, the sequence of conformational tran

158 Minimum free energy (MFE) predictions are known to be "ill condi

159 lude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for con

160 The characterization of the free-energy minima identified on this FES proposes a bin

161 here the system progressively explores lower free-energy minima which are either amorphous (ageing) o

162 r can compute the secondary structures using free energy minimization algorithm in terms of RNAfold t

163 Swellix provides a practical alternative to free energy minimization tools when multiple structures,

164 This process is driven by the interfacial free energy minimization, which gives rise to a breakup

165 We find that the global free energy minimum corresponds to A-A pairs stacked ins

166 ameters that compose the 2004 version of the free energy nearest neighbor rules.

167 lations between the theoretically calculated free energies of activation and kexp for 31 reactions of

168 Free energies of activation for all elementary reactions

169 Computed free energies of activation reproduce the preference for

170 not significantly lower the computed overall free energies of activation.

171 ative versus native interactions, we compute free energies of association of various combinations of

172 de theoretical estimates of aqueous standard free energies of formation for inorganic chloramines, br

173 based on high-accuracy theoretical standard free energies of formation in gas phase combined with qu

174 e findings in the context of the aggregation free energies of longer peptides that are able to form a

175 Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL op

176 relationship quantum mechanically calculated free energies of reaction and the literature-reported ex

177 Gibbs free energies of reactions with various free radicals in

178 le originally developed for relative binding free energies of small molecules to proteins and not spe

179 endent manner given reasonable values of the free energies of specific and non-specific DNA binding a

180 energy simulations reveal that the relative free energies of the flipped Gln conformation and the fl

181 ides a comprehensive data set describing the free energies of the neutral inorganic halamines, the an

182 The free energies of the reactions vary over more than 90 kc

183 ic square scheme reveals a bond dissociation free energy of 71.7 +/- 1.1 kcal mol(-1) for the hydrope

184 We analyze the definition of the Gibbs free energy of a nanoparticle in a reactive fluid enviro

185 lar dynamics method to calculate the binding free energy of a series of alpha-ketoamide analogues rel

186 ation that enables the enzyme to harness the free energy of ADP binding to drive ATP release.

187 ion, a prototypical chaotrope, determined a free energy of adsorption within error of that for air/w

188 modes and ranks them based on the calculated free energy of alpha-helix association.

189 hydrogen bonds are major contributors to the free energy of association of GxxxG-mediated dimers.

190 has a similar dissociation constant (Kd) and free energy of association to the Vpu homooligomer.

191 ion to its helicase activity, eIF4A uses the free energy of ATP binding and hydrolysis as a regulator

192 veals a dramatic, enthalpy-dominated gain in free energy of binding resulting in a factor of 41000 in

193 vel recognition mechanisms and calculate the free energy of binding the hypothesized ligands to YKL-4

194 the monolayers are directly related to their free energy of binding to ice.

195 elf-shedding; (2) the release of the surface free energy of condensate promotes the self-shedding.

196 to long-range interactions that minimize the free energy of distorted regions.

197 of the intrinsic ligand-binding affinity and free energy of each integrin conformational state on the

198 n ionic potential and the enthalpy and Gibbs free energy of formation for previously measured oxyanio

199 The activation enthalpy and free energy of inactivation indicated an endothermic rea

200 Neither the free energy of miR159-target complementarity, nor miRNA

201 Fe(I), and Fe(II) complexes reveals that the free energy of N2 binding across three oxidation states

202 cO) is a transmembrane protein that uses the free energy of O2 reduction to generate the proton conce

203 d domain organization due to favorable Gibbs free energy of phospholipid mixing.

204 This model connects the activation Gibbs free energy of point defects formation and migration wit

205 The unfolding free energy of the consensus-HD is 5 kcal.mol(-1) higher

206 y thermodynamic manner, i.e. by lowering the free energy of the native state and with almost no effec

207 is the thermodynamic parameter that sets the free energy of the oligomers.

208 rug additively and independently reduces the free energy of the open receptor compared with the close

209 in the confined geometry that minimizes the free energy of the system.

210 ative state and with almost no effect on the free energy of the transition state.

211 This reciprocal behavior shows that the free energy of the TSA, with all ligands bound, is lower

212 The free energy of water-to-interface amino acid partitionin

213 ology to measure resting affinities (binding free energies) of these and other agonists in adult-type

214 The independence of the conformational free energies on solvent polarity, polarizability, and H

215 RV RNA ensemble that do not occur in minimum free energy or centroid predicted structures.

216 We have also determined the lowest free-energy path between two longest-lived metastable st

217 m quantum-chemical calculation of the lowest free-energy pathway, this approach can be misleading whe

218 To prove the concept, we employed free energy perturbation (FEP) coupled with lambda-excha

219 Here, we describe a systematic free energy perturbation (FEP) protocol and calculate th

220 ar dynamics simulations (Antibodyomics7) and free energy perturbation analyses (Antibodyomics8) provi

221 Molecular dynamics free energy perturbation has been employed to systematic

222 using molecular dynamics simulations and the free energy perturbation method (MD/FEP) in fragment opt

223 In this work, we show that FEP+, which is a free energy perturbation method based on all-atom molecu

224 estigation of the ability of our most recent free energy perturbation methodology to model the thermo

225 In addition, using molecular dynamics and free energy perturbation simulations, we elucidate the e

226 Free energy perturbation theory, employing all-atom and

227 se changes, we used molecular simulation and free-energy perturbation approaches to identify probable

228 resources and algorithms and that alchemical free energy predictions methods are close to becoming a

229 At the same concentration, the aggregation free energy profile of Abeta42 is more downhill, with a

230 We predict the electronic free energy profile of the competing states, and the the

231 The free-energy profile for interconversion between conforma

232 concentration, although the grand canonical free energy profiles are uphill for HTT exon 1 fragments

233 urately, with which depth-dependent transfer free energy profiles can be derived.

234 The calculated free energy profiles capture a discrete pattern in the r

235 Free energy profiles corresponding to the unfolding of T

236 erimental data and confirm that the computed free energy profiles indeed reproduce the observed selec

237 The free energy profiles obtained for the pathways leading t

238 ations for both the potential energy and the free energy profiles showed very similar geometric featu

239 elay from Tyr21 to the flavin via Gln63, the free-energy profiles for Gln63 rotation were calculated

240 r dynamics simulations that characterize the free-energy profiles of explicit proton transport throug

241 n and thereby obtain the diffusivity and the free-energy profiles of the drug as a function of skin d

242 A linear free energy relationship between acid pKa and second-ord

243 We find a linear free energy relationship between the Hammett para substi

244 erence electrophiles according to the linear free energy relationship log k2(20 degrees C) = sN(N + E

245 A linear free energy relationship was established to offer a pred

246 Our calculations provide a linear free energy relationship, with slope 0.8, between the ac

247 e(II)/Fe(total) and is described by a linear free energy relationship.

248 rence electrophiles, according to the linear-free-energy relationship log k2 (20 degrees C) = sN (E +

249 We found a linear free-energy relationship quantum mechanically calculated

250 The model uses polyparameter linear free energy relationships (pp-LFERs) to estimate the par

251 Moreover, two polyparameter linear free energy relationships were developed for the adsorpt

252 have facilitated a detailed study of linear free energy relationships, kinetic isotope effects, and

253 s deprotection methodology derived by linear free-energy relationships (LFER), quantum theory of atom

254 Kinetic studies and linear free-energy relationships reveal that the initiation ste

255 isotope effects ((2)H, (10)B, (13)C), linear free-energy relationships, and density functional theory

256 reducing quinone (Q), complex I employs the free energy released in the process to thermodynamically

257 Free energy requirements for activation are defined with

258 Free energy scaling analysis and molecular dynamics simu

259 OM2/CHARMM free energy simulations for the SpnF-catalyzed reaction

260 Free energy simulations reveal that the relative free en

261 mechanics (QM/MM) calculations combined with free energy simulations show that the Diels-Alder pathwa

262 hybrid quantum mechanics-molecular mechanics free energy simulations with the Met(20) loop in a close

263 Using a combination of free energy simulations, single-pair Forster resonance e

264 neering channel stoichiometry and performing free energy simulations.

265 Molecular dynamics and free-energy simulations confirm designation of NaVAb/1-2

266 Free-energy simulations elucidate the active site confor

267 with systematic, in silico Alanine scanning free-energy simulations, which indicate that the major c

268 uilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machin

269 y support a hypothesis that the low absolute free-energy state is the desensitized state of the intac

270 The lowest free-energy structure had a root mean square deviation o

271 Frank-Kasper phases, have nearly degenerate free energies, suggesting that processing history drives

272 for the computation of the multidimensional free-energy surface (FES) describing the protein-ligand

273 s (MetaD) to characterize the conformational free-energy surface of [Formula: see text] The focus of

274 Molecular dynamics and free-energy surface studies indicated that Asp-168 is im

275 of a comprehensive picture of the underlying free energy surfaces and the corresponding dynamics of n

276 ogenase, by calculating potential energy and free energy surfaces using two different Combined Quantu

277 ating the exploration of uncharted effective free-energy surfaces (FESs).

278 Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; s

279 on of determination of unfolding mechanisms, free energies, temperatures, and heat capacity differenc

280 Transfer free energies (TFEs) of residues in the transmembrane (T

281 or the calculation of protein-ligand binding free energies, the challenges associated with these meth

282 tability are benchmarked against DFT-derived free energies; their details are essential to design hos

283 Biomolecular machines consume free energy to break symmetry and make directed progress

284 ion of oxygen to water and uses the released free energy to pump protons against the transmembrane pr

285 The breakup causes the electric current free energy to reduce in some cases.

286 REC phosphorylation coordinately impart the free energy to shift PhyR to an open, active conformatio

287 y overlaps with the ribosomal footprint, the free energy to unfold only the overlapping structure con

288 firming an essential yet neglected aspect of free energy transduction and suggesting the potential ge

289 ptide via cation-pi interactions, but linear free energy trends suggest they do not contribute equall

290 reason for the higher DeltaG degrees (5), or free energy, value seen for Open-J at low salt.

291 mechanical prediction of the structures and free energies, we show that the presence of a thin subox

292 one can assume that there is a well-defined free energy well around the native state, which makes th

293 ard inactive states of HCN4 and broadens the free-energy well of the apo-form, enhancing the millisec

294 ntials of mean force show several attractive free energy wells distinguished by numbers of intervenin

295 Over 160 experimental conformational free energies were measured in 13 different solvents to

296 d apices provide the majority of the binding free energy, while charged residues elsewhere are less c

297 The activation free energies with ethylene or acetylene range from 11.8

298 luating protein structures requires reliable free energies with good estimates of both potential ener

299 We find an enormous range of hydrogen bond free energies, with some weaker than water-water hydroge

300 re growth rate defect on substrates with low free energy yields and at elevated temperatures (39 degr