ライフサイエンスコーパス: potential of mean force

1 we identified in terms of a two-dimensional potential of mean force.

2 ibutions may be represented by a single pair potential of mean force.

3 l based on minimization of a knowledge-based potential of mean force.

4 in order to predict the stability using the potential of mean force.

5 otein receptor is formulated on the basis of potentials of mean force.

6 free energies are replaced with appropriate potentials of mean force.

7 O, and cyclohexane using novel 3-dimensional potentials of mean force (3-D PMF) calculations coupled

8 mulations to calculate the three-dimensional potentials of mean force (3D-PMFs) for a Na+ cation and

9 by making use of two conformational database potentials of mean force: a nucleic acid torsion angle d

10 from the variations in the voltage-dependent potential of mean force along a reaction path connecting

11 gy and irreversible work, we reconstruct the potential of mean force along the conduction pathway thr

12 ing a single ion into the channel, i.e., the potential of mean force along the permeation pathway.

13 ut a 3-methyl adenine by AlkD and computed a potential of mean force along this path to delineate the

14 We report potentials of mean force along a root-mean-square-distan

15 Potentials of mean force along the reaction coordinate f

16 Mechanistic insights gained by a potential of mean force analysis implicated that the dru

17 ted annealing using a torsion angle database potential of mean force and compared to those deduced by

18 hrough the gramicidin pore is described by a potential of mean force and diffusion coefficient obtain

19 approximate the effects of solvent through a potential of mean force and therefore make solvated simu

20 ong enough for the extraction of a separable potential of mean force and wet-to-dry transitions.

21 f structural analogues on the basis of their potentials of mean force and calculated unbinding energi

22 ine (oxoG) DNA glycosylase MutM, a series of potentials of mean force and thermodynamic integration s

23 ce threading (SST) method (that uses complex potentials of mean-force) and also to a multiple sequenc

24 ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution

25 otentially useful for determining the forms, potentials of mean force, and time dependence of functio

26 The strength and shape of the potential of mean force are in conflict with earlier cla

27 the fact that unlike the free energies, the potentials of mean force are not in general homogeneous

28 tal "data" toward an improved theory for the potential of mean force as required for optimum design o

29 The potential of mean force associated with the dimerization

30 The potential of mean force associated with the resulting un

31 of these peptides, and compute high-accuracy potential of mean force association curves.

32 The calculated potential of mean force at the PM3/CHARMM level supports

33 at the time-determining step is crossing the potential-of-mean-force barrier.

34 pidly relaxing dynamic bends within a single potential-of-mean-force basin.

35 lexes has grown to the point were rederiving potentials of mean force becomes meaningful for statisti

36 as that of the solvent-mediated part of the potential of mean force between a pair of solute molecul

37 The obtained potential of mean force between folded lysozyme molecule

38 Our calculations of the potential of mean force between proteins and protein clu

39 We could then determine the potential of mean force between the flavin and the tyros

40 pressure is investigated by calculating the potential of mean force between them at constant pressur

41 utationally efficient method to evaluate the potential of mean force between two folded protein molec

42 By calculating the potential of mean force between two solvated graphene sh

43 The potential of mean-force between the adsorbing protein an

44 Furthermore, our calculations of the potentials of mean force between the H4 tail and a DNA f

45 ata are complemented by NMR measurements and potentials of mean force between the peptides, calculate

46 Potentials of mean force calculated for the diffusion of

47 ment with free energy changes derived from a potential of mean force calculation and indirect experim

48 inding conformations were extracted from the potential of mean force calculation and were subjected t

49 The short timescale of the potential-of-mean-force calculation precludes the inclus

50 The potential of mean force calculations along the ammonia t

51 Detailed potential of mean force calculations along the putative

52 Potential of mean force calculations along the transfer

53 s for egress of a bromide ion obtained using potential of mean force calculations are in good agreeme

54 Potential of mean force calculations find no free-energy

55 pproach to traditional MD simulations and/or potential of mean force calculations for: (i) characteri

56 Potential of mean force calculations have been performed

57 Specifically, potential of mean force calculations reveal that in the

58 Potential of mean force calculations show how the recove

59 iple nucleotide states, and through rigorous potential of mean force calculations, compute the free e

60 ined molecular dynamics (MD) simulations and potential of mean force calculations, we have explored t

61 icit lipid bilayers coupled to thermodynamic potential of mean force calculations.

62 entally are reproduced within fivefold using potential of mean force calculations.

63 ted PDI dimer in water is investigated using potential of mean force calculations.

64 tron paramagnetic resonance spectroscopy and potential-of-mean force calculations on the isolated TM

65 Potential-of-mean-force calculations identify thermodyna

66 w-skeletal (ssTnC or TnC1b) paralogs through potential-of-mean-force calculations.

67 The potential of mean force characterizing glycerol in the c

68 can be easily computed from protein-crowder potential of mean force, corrects for the penetrability

69 The energy functions included 13 pairwise potentials of mean force, covering a wide range of funct

70 onpolarizable) force fields to calculate the potential of mean force defining the equilibrium flux of

71 this paper, we describe the derivation of a potential of mean force derived from all high-resolution

72 The landscape is mapped out by potentials of mean force derived from replica-exchange m

73 tion energies, the modified Tanford-Kirkwood potential of mean force differs from a computationally i

74 The resulting potential of mean force distributions show a fine struct

75 ound that the energetic contributions to the potential of mean force do not change appreciably when t

76 tact potentials, knowledge-based potentials, potentials of mean force, etc.).

77 Rigid-body modeling and potential of mean force evaluations show that the cholin

78 rom the aqueous phase into the membrane; the potential of mean force exhibits highly favorable free e

79 ascent-chain folding, we have calculated the potential of mean force for alpha-helix formation of a 1

80 The potential of mean force for dragging the particle throug

81 The potential of mean force for each compound through a 1,2-

82 out free energy calculations to compute the potential of mean force for the cagelike silicate polyio

83 d combined with the WHAM method provided the potential of mean force for the hydride transfer process

84 etical model is proposed, which computes the potential of mean force for the nucleophilic aromatic su

85 The potential of mean force for the proton adsorption to the

86 We construct the profile of potential of mean force for the unbinding of PIIIA from

87 these unbinding pathways, we calculated the potentials of mean force for acetylcholine unbinding.

88 tripeptides and sulfated protein complexes, potentials of mean force for interacting residue pairs,

89 We derive potentials of mean force for six different solutes perme

90 This article reconstructs potentials of mean force for the conduction of ammonia t

91 zynski's equality were used to construct the potential of mean force from multiple pulling trajectori

92 We have performed a comparison between the potentials of mean force governing the translocation of

93 Calculation of the potential of mean force (i.e., free energy profile) of c

94 We used this potential of mean force in a generalized Poisson-Boltzma

95 in the 298-1000 K range reveal an attractive potential of mean force in the extended chain region of

96 We find that the potential of mean force in the phi(psi) plane is markedl

97 The resulting approximate potentials of mean force indicate that the PLN pentamer

98 Analysis of potentials of mean force indicates that the double-stran

99 Analysis of potentials of mean force indicates that the tendency of

100 The potential of mean force is calculated for the water and

101 ditional K(+) in the pore, and the three-ion potential of mean force is computed using extensive all-

102 ch is an umbrella sampling technique where a potential of mean force is determined by pulling the lig

103 The effective electrostatic potential of mean force is expressed in terms of adjusta

104 The potential of mean force obtained by SCC-DFTB/MM simulati

105 The low potential of mean force obtained is consistent with the

106 Potentials of mean force obtained from the two surfaces

107 ar, umbrella sampling was used to obtain the potential of mean force of 4-cyano-4'-pentylbiphenyl (5C

108 vides complete three-dimensional maps of the potential of mean force of gas ligand placement anywhere

109 Comparison of the potentials of mean force of NaK-CNG and K(+)-selective c

110 liquid structure, were used to calculate the potential of mean force on a single ion.

111 on behaviors, is assessed by calculating the potential of mean force or dimerization free energy of t

112 barrier of 3.1 kcal/mol (calculated via the potential of mean force) or 3.4-3.5 kcal/mol (rigid barr

113 From this analysis, two potential-of-mean-force parameters, the effective monome

114 To address this issue, we carried out potential of mean force (PMF or free energy profile) cal

115 Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO m

116 yzed the results based on the combination of potential of mean force (PMF) and stress field calculati

117 eparated configurations in the solute-solute potential of mean force (PMF) are stabilized with respec

118 ne helix association, we have calculated the potential of mean force (PMF) as a function of helix-hel

119 , assuming that the difference in the proton potential of mean force (PMF) between gA and its analogs

120 ctions are consistent with umbrella sampling/potential of mean force (PMF) calculations as a function

121 Potential of mean force (PMF) calculations confirm that

122 Potential of mean force (PMF) calculations utilizing the

123 ating modes have also been investigated with potential of mean force (PMF) calculations.

124 rmational energetics of this peptide using a potential of mean force (PMF) consisting of the AMBER/OP

125 We investigate methods for extracting the potential of mean force (PMF) governing ion permeation f

126 The specification of the corresponding potential of mean force (PMF) is based on a defined set

127 simulations were performed to construct the potential of mean force (PMF) of the ligand and calculat

128 rella-sampling calculations to calculate the potential of mean force (PMF) profiles for translocation

129 Revisiting potential of mean force (PMF) scoring, we present an upd

130 d the scope of those studies by carrying out potential of mean force (PMF) simulations to determine t

131 Potential of mean force (PMF) simulations with a hybrid

132 To begin to understand ion permeation, the potential of mean force (PMF) was calculated for displac

133 the first application of a method based on a potential of mean force (PMF) with restraining potential

134 he molecule close to DNA as indicated by the potential of mean force (PMF).

135 Consistent potentials of mean force (PMF) are obtained for the spin

136 Potentials of mean force (PMF) between all possible ioni

137 Potentials of mean force (PMF) calculations along the en

138 eaction are elucidated using two-dimensional potentials of mean force (PMF) derived from free energy

139 on are elucidated here using two-dimensional potentials of mean force (PMF) derived from free-energy

140 ular dynamics were employed to calculate the potentials of mean force (PMF) for a variety of restrain

141 rdinate was used to calculate the individual potentials of mean force (PMF) for flipping of the Watso

142 eaction are elucidated using two-dimensional potentials of mean force (PMF) simulations utilizing fre

143 in the experimental literature, the computed potentials of mean force (PMF) suggest that the proton t

144 ction energies of protein-ligand atom pairs (potentials of mean force, PMF).

145 ella sampling simulations and calculated the potentials of mean force (PMFs) as a function of TM heli

146 This parameter optimization is guided by the potentials of mean force (PMFs) between amino acid polar

147 The potentials of mean force (PMFs) between two methane mole

148 force simulations allowed us to reconstruct potentials of mean force (PMFs) for chloride and sodium

149 We calculate potentials of mean force (PMFs) for the intermolecular i

150 lipid bilayer by computing the corresponding potentials of mean force (PMFs) using fully atomistic mo

151 le mechanisms have been computed in terms of potentials of mean force (PMFs) within hybrid QM/MM pote

152 f Poisson-Nernst-Planck (PNP) theory, termed Potential-of-Mean-Force-Poisson-Nernst-Planck theory (PM

153 ce calculations are employed to estimate the potential of mean force profiles associated with transpo

154 Calculation of the potential of mean force profiles for the initial separat

155 ype and the mutants is the result of altered potential of mean force profiles that are dominated by t

156 y in the GLIC channel by the construction of potential-of-mean-force profiles for sodium and chloride

157 Potential of mean force quantum mechanical/molecular mec

158 The potential of mean forces recapitulate a higher stability

159 coordinating ligands coupled to an effective potential of mean force representing the influence of th

160 part and the motion of the particles in the potential of mean force resulting from the intermolecula

161 alculated distance and orientation-dependent potentials of mean force show several attractive free en

162 In this study, we analyze the potential of mean force, showing that a simplified six-s

163 y parallels a key intermediate observed in a potential of mean force-simulated dissociation pathway o

164 penalty, calculated from molecular dynamics/potential of mean force simulations, for the conformatio

165 ecifically, we performed molecular dynamics, potential-of-mean force simulations to obtain the free e

166 The reported potential of mean force suggests that the nanoparticle c

167 culated by means of free energy perturbation potential of mean force techniques by using appropriate

168 tein interface, and a torsion angle database potential of mean force to bias interfacial side chain c

169 are used to derive one- and two-dimensional potentials of mean force to examine specific reaction pa

170 c tethers and variations in the shape of the potential of mean force were considered.

171 We calculate the potential of mean force, which gives us an estimate of t

172 underwent spatial diffusion along a bistable potential of mean force, with electrostatic forces coupl

173 A comparison of the potentials of mean force yields a number of important re