ライフサイエンスコーパス: conformational space

1 form, such that it is able to sample a broad conformational space.

2 of success when the user widely explores the conformational space.

3 ompact structures and reduces the accessible conformational space.

4 orders of magnitude smaller than their full conformational space.

5 of the htel quadruplexes and restrict their conformational space.

6 be used to drive the search toward relevant conformational space.

7 nel the enzyme through functionally relevant conformational space.

8 que able to probe lowly populated regions of conformational space.

9 TCA motif allows it to sample a much greater conformational space.

10 ensembles to converge on a stable 2D map of conformational space.

11 small, yet complex sub-spaces of a protein's conformational space.

12 ethodology samples all relevant parts of the conformational space.

13 ng and therefore on the substructures of the conformational space.

14 , which greatly enhances the sampling of the conformational space.

15 reading frame by restricting anticodon loop conformational space.

16 ontacts within a highly restricted subset of conformational space.

17 refoil, and are juxtaposed to one another in conformational space.

18 with replica exchange Monte Carlo to explore conformational space.

19 tational effort, considering the size of the conformational space.

20 e two hybrids populated different degrees of conformational space.

21 increase involved in direct searches of the conformational space.

22 this same loop by restricting the accessible conformational space.

23 ergy conformation of the backbone segment in conformational space.

24 This guest has almost no effect on the conformational space.

25 that detects regions of interest in protein conformational space.

26 e free energy surface maps of their complete conformational space.

27 ially allows a systematic exploration of the conformational space.

28 eric site and samples a significantly larger conformational space.

29 der parameters as a method for exploring RNA conformational space.

30 ong a curved pathway in the high-dimensional conformational space.

31 mes a stepwise and mutual reduction of their conformational space.

32 s to dramatically increase their sampling of conformational spaces.

33 s it requires an extensive sampling of their conformational spaces.

34 tween the folded and unfolded regions of the conformational space; 2), observed nonnative stacking an

35 ansion in the absence of solvent to sample a conformational space 3-5 fold broader than in solution.

36 To sample the conformational space, a biasing force is introduced that

37 odule and form a cross-link that reduces the conformational space accessed by the enzyme, facilitatin

38 orm an extensive comparative analysis of the conformational space accessed upon ligand binding, and i

39 activity, indicating that modulation of the conformational space accessible for the two bonds depart

40 ng trajectories have extensively sampled the conformational space accessible to B-DNA at room tempera

41 of conformational entropy and the volume of conformational space accessible to HCDR3 in the ligand-f

42 Restriction of the conformational space accessible to the basic region may

43 raph sampling/data mining approach to reduce conformational space and accelerate global sampling of c

44 es of the hybrid material nearly doubles its conformational space and accessible surface area.

45 ein (IDP) conformers occupy large regions of conformational space and display relatively flat energy

46 ence space, but suffer from undersampling of conformational space and energy function inaccuracies.

47 e demonstrated by computing the reduction in conformational space and entropy due to naturally modifi

48 lexes contain residual water molecules whose conformational space and hydrogen-bond formation ability

49 he unfolded state, imino acids both restrict conformational space and present cis-trans isomerization

50 method that exhaustively samples side chain conformational space and rigorously calculates multibody

51 onfiguration, the ability to rapidly explore conformational space and sample conformations of complex

52 ixtures based on the characterization of the conformational space and the assignment of chemical form

53 The analysis identified the conformational space and the sequence requirement of Cal

54 nd biological implications of the accessible conformational space and the suggested transition pathwa

55 This method permits efficient sampling of conformational space and yields precise estimates of fre

56 for the power of the OSRW method in sampling conformational space and, hence, in providing quantitati

57 It is mostly due to the size of protein conformational spaces and required simulation time scale

58 hat can rapidly sample the vast sequence and conformational space, and a scoring function that can id

59 ion, models of energy functions, sampling of conformational space, and applications in the modeling o

60 y usually suffer from incomplete sampling of conformational space, and become prohibitively expensive

61 Simulations efficiently sample conformational space, and complete folding trajectories

62 ge molecular dynamics is used to explore the conformational space, and discrete path sampling is empl

63 based methods, how they divide up and search conformational space, and how they evaluate candidate co

64 etween a macrocycle's shape persistence, its conformational space, and the resulting functions.

65 restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bon

66 The conformational space annealing (CSA) method for global o

67 lves a search of conformational space by the conformational space annealing (CSA) method, followed by

68 tion of the Onsager-Machlup action using the conformational space annealing (CSA) method.

69 alphaBB, and a stochastically based method, conformational space annealing (CSA).

70 the conformational space with the use of the conformational space annealing method and the newly opti

71 physics-based UNRES energy function and the conformational space annealing method of global optimiza

72 a training set of 24 complexes, explores the conformational space around the whole receptor without r

73 the LR, any particular NS1 could sample the conformational space around these states to engage ED in

74 nal ensemble is required to cover the entire conformational space as much as possible rather than to

75 ure prediction often randomly sample protein conformational space as opposed to experimentally sugges

76 mations that reveals a dramatic reduction of conformational space as sampled by experimentally observ

77 with the chain undergoing some searching of conformational space as the threading takes place.

78 interactions is challenging due to the vast conformational space associated with interactions of hig

79 ces within triplet repeat domains expand the conformational space available for selection and targeti

80 e structure, which also strongly affects the conformational space available in the N-terminal region

81 kinases acts as a "wedge" that restricts the conformational space available to key regions in the kin

82 These findings imply that the conformational space available to simple peptide-based c

83 constructs placed substantial limits on the conformational space available to the analogues relative

84 able to play an active role in reducing the conformational space available to the folding chain, or

85 risons, we briefly discuss insights into the conformational space available to the hammerhead ribozym

86 ed in the fibrillar state and thus limit the conformational space available to the polypeptide chains

87 This construct reduces the conformational space available to these repetitive DNA s

88 in the RNA that maximally sample suboptimal conformational space based on the ensemble's partition f

89 tional approaches, they explore not only the conformational space but also the space of possible sear

90 tides transiently populate the alpha-helical conformational space, but the S20P peptide, which does n

91 cluded volume constraints reduce the size of conformational space by many orders of magnitude, the nu

92 al constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and s

93 includes equilibrium sampling of the peptide conformational space by simulated tempering dynamics wit

94 inding and sequence-dependent alterations of conformational space by structural analysis of all relev

95 hierarchical procedure involves a search of conformational space by the conformational space anneali

96 sample the catalytically relevant region of conformational space, can reproduce the available data.

97 aughter genes selectively restricted protein conformational space, causing this dual DNA-binding spec

98 some parts of the molecules into regions of conformational space close to the bound state (or give i

99 developed protocol that ensures that all of conformational space, consistent with the structural con

100 e is biased toward productive regions in the conformational space determined by the native structure.

101 , while the 18- and 24-chain models sample a conformational space different from the crystalline stru

102 e enzyme and demonstrate that motions in the conformational space do not help drive catalysis.

103 pecific construction rules that restrict the conformational space drastically, it should be possible

104 in vitro model study is aimed at probing how conformational space evolves for purified N-terminal pol

105 Consequently, conformational space expands under folding conditions, a

106 We show that IDPs undergo a vast conformational space expansion in the absence of solvent

107 nteraction frees P2 and thereby enhances the conformational space explored by the undocked attached P

108 t we lack general insight into the extent of conformational space explored, and specifically the prop

109 etase, suggesting that their sampling of the conformational space facilitates their recognition by th

110 Analysis of the conformational space for (His-Ala-Ile + H)(+) precursor

111 ix, which results in an improved sampling of conformational space for a given computational effort.

112 Our method creates a stable map of conformational space for a given RNA sequence.

113 t topological constraint not only limits the conformational space for effective switching between fun

114 n a physical interaction model, a simplified conformational space for efficient enumeration, and an e

115 ers that are thought to represent the entire conformational space for nine training set molecules, co

116 The conformational space for Phe228 is severely limited by t

117 s the nascent peptide to compact and explore conformational space for potential tertiary folding part

118 0.98A) exhibited a significantly restricted conformational space for the anticodon loop in compariso

119 r and outer domain to explore the accessible conformational space for the bridging sheet.

120 The f(5)C(34) defined a reduced conformational space for the nucleoside, in what appears

121 However, adequate exploration of conformational space for these highly dynamic molecules,

122 he importance of simulation time in sampling conformational space for this topology.

123 l Optimization Program (PLOP), which samples conformational space from first principles to build sets

124 ver starts by efficiently searching the vast conformational space from only the loop sequence informa

125 We have mapped protein conformational space from two to seven residue lengths b

126 erform near-complete search of the symmetric conformational space in a very short time.

127 Our data show that LmrA samples a very large conformational space in its apo state, which is signific

128 ere the results of exhaustively sampling the conformational space in protein-protein association usin

129 opulating the alpha-region of the (phi, psi) conformational space in the regions corresponding to the

130 paper, the hypothesis that limited access to conformational space is a requirement for protein hinges

131 ltiple start conformations, it is shown that conformational space is covered adequately and that the

132 ate description of chemical structures in 3D conformational space is difficult due to the high-dimens

133 This funneling of the available conformational space is encoded within the SH3-SH2 conne

134 ull-size and truncated mutants explore their conformational space is examined in terms of the mean-sq

135 The magnitude of protein conformational space is over-estimated by the traditiona

136 The eight-dimensional conformational space is presented as a series of two-dim

137 The conformational space is searched extensively at the unit

138 In order adequately to sample conformational space, methods for protein structure pred

139 l, we find that the flexible loop explores a conformational space much larger than in the MD trajecto

140 Using a conformational space network representation of the L1L s

141 g step passes through a narrow region of the conformational space network, whereas the allosteric act

142 These studies suggest that the conformational space occupied by a glycan can play an im

143 dness of RNA folding landscapes extends into conformational space occupied by native conformations.

144 The simulations show that the conformational space occupied by TcdB bound to the two p

145 tricyclic core of Delta (8)-THC and that the conformational space occupied by the C3 substituents inf

146 A global conformational space of 6253 dinucleoside monophosphate

147 sed understanding of the degree to which the conformational space of a ligand is restricted upon bind

148 needs to be induced or pre-exists within the conformational space of a monomeric CA.

149 esidues, imposes powerful constraints on the conformational space of a protein.

150 mentally alters the energetically accessible conformational space of a thiomannoside when bound withi

151 ture of multiple states (VMMS) to sample the conformational space of all chemical states simultaneous

152 The conformational space of aspirin is spanned by three inte

153 e de novo algorithm exploited the restricted conformational space of disulfide bonds (Cys14-Cys38, Cy

154 Here the gas phase conformational space of drug and drug-like molecules has

155 molecular dynamics simulations to sample the conformational space of each protein.

156 The conformational space of feasible RNA secondary structure

157 ns of the different GFP mutants modulate the conformational space of flexible parts of the protein.

158 ionalize this peculiar regioselectivity, the conformational space of humulene has been explored compu

159 mulations were used as a means to sample the conformational space of ligands to include all accessibl

160 By considering a reduced conformational space of local optimal stack configuratio

161 f predicted structural models to the allowed conformational space of longer fragments is a significan

162 as been developed recently for searching the conformational space of macromolecules.

163 (TAMD) in collective variables to sample the conformational space of multidomain proteins in all-atom

164 sent a new algorithm to efficiently mine the conformational space of multiple actives and find small

165 tein might be responsible for the restricted conformational space of N-glycan chains.

166 the difficulties of adequately sampling the conformational space of polynucleotides, we used coarse-

167 tural preferences of backbone and side chain conformational space of polypeptide chains in a united-r

168 e to their ability to capture the continuous conformational space of protein structures.

169 data, they do not enable the sampling of the conformational space of proteins with correct statistica

170 n provide an effective representation of the conformational space of proteins.

171 simulations can comprehensively explore the conformational space of proteins.

172 Characterizing the conformational space of such complexes is challenging: i

173 ked Delaunay analysis, an examination of the conformational space of TcdB in its apo form as well as

174 The conformational space of the 10-55 fragment of the B-doma

175 This modulation of the conformational space of the 26S proteasome by Ubp6 expla

176 molecular dynamics simulations to sample the conformational space of the Abeta monomer and constructe

177 thylation of the peptide bond constrains the conformational space of the amino acid and eliminates th

178 gned and synthesized in order to explore the conformational space of the C-3 pharmacophore.

179 Here we report on the conformational space of the Cro dimer in solution using

180 accompanies any significant reduction in the conformational space of the denatured state.

181 sented in terms of isoenergy contours in the conformational space of the glycosidic (chi) and C4'-C5'

182 Systematic exploration of the conformational space of the ligand combined with molecul

183 , pSer133 appears to restrict the accessible conformational space of the loop region and thus reduces

184 ed state and the environment, we explore the conformational space of the N-terminal 1-5 fragment of b

185 hallenged this proposal by investigating the conformational space of the N-terminal POTRA domains of

186 l reaction coordinate was used to sample the conformational space of the peptide.

187 an otherwise hidden structure in the complex conformational space of the peptide.

188 We further show that modeling the conformational space of the reactant and the transition

189 consideration, thus sampling adequately the conformational space of the receptor, even in cases of l

190 dary structure strongly limit the accessible conformational space of the ribozyme, and that these so-

191 d of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+)

192 eral ethylene glycol moieties may reduce the conformational space of the substituents in an oligonucl

193 r dynamics trajectories had sampled the full conformational space of the system.

194 Thus, the conformational space of these RNAs is largely determined

195 We explore the conformational space of this protein-DNA complex using m

196 The conformational space of TM2 helices was found to differ

197 is context, mapping the changes in available conformational space of transcription intermediates duri

198 molecular dynamics simulations to sample the conformational space of various oligomerization states a

199 I consider conformational spaces of tRNA(phe) defined by sets of su

200 side chain may not sample the full range of conformational space once thought.

201 Very high temperatures narrow the conformational space presented by both Ubiquitin and Con

202 ordered proteins, where the sampling of vast conformational space presents a serious problem.

203 contacts place additional constraints on the conformational space, progressively funneling the molecu

204 Efficient exploration of protein conformational space remains challenging especially for

205 lowing for quasi-equilibrium sampling of the conformational space restricted by the ribosome.

206 The mapping of the conformational space reveals nine primary clusters which

207 appear to constrain rRNA secondary-structure conformational space: ribosomal proteins and rRNA sequen

208 e-based approach is presented to explore the conformational space sampled by a multidomain protein sh

209 We also show that Zn(II) binding limits the conformational space sampled by CzrA and causes the elec

210 on is performed via overlap integrals of the conformational space sampled by ligands with respect to

211 permit one to obtain a detailed view of the conformational space sampled by the dodecamer in solutio

212 Here, we determine the conformational space sampled by the multidomain splicing

213 we obtain a quantitative description of the conformational space sampled by the N-terminal domain re

214 A detailed view of the conformational space sampled by the RNAP and the molecul

215 The conformational spaces sampled by the loop region and by

216 Glycan binding constrained the conformational space sampling by the HA.

217 it and explicit solvent simulations, and the conformational space sampling is carried out with a high

218 els, affording systematic enhancement of the conformational space sampling of the protein.

219 nuclei, improve substantially with enhanced conformational space sampling up to an optimal accelerat

220 cking, their structural design minimizes the conformational space searched in the diffusion process.

221 ation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen

222 bors and can restrict the size of accessible conformational space significantly.

223 ta we show that the core ensemble occupied a conformational space similar to that observed under expe

224 tter suited to appropriately explore protein conformational space than those from other CG methods at

225 likely represent a realistic sampling of the conformational space that an antibody explores in aqueou

226 ent sampling and can also suggest subsets of conformational space that are more consistent with exper

227 ccurring amino acids, limiting the degree of conformational space that can be surveyed.

228 de bonds were designed, covering a promising conformational space that could not be reached by the na

229 Our structures provide insights into the conformational space that EF-G samples on the ribosome a

230 ding by decreasing the dimensionality of the conformational space that has to be searched.

231 absence of any ligand, samples an extensive conformational space that includes breathing of the orth

232 otocol implements a multisteps search in the conformational space that is driven by iteratively minim

233 provide clear structural motifs and identify conformational space that is important for cytotoxicity.

234 The 36-chain model stays in a conformational space that is very similar to the initial

235 20ns), which greatly reduces the size of the conformational space that needs to be explored in search

236 anism of glutamate receptors and the complex conformational space that the LBD layer can sample.

237 Although the pathways differed in conformational space, the physical properties of the con

238 a-theta plots for intuitive visualization of conformational space, the pseudotorsional convention des

239 d plausible mechanisms for reducing the vast conformational space through distinct ensembles of struc

240 hemselves sufficient to reduce the effective conformational space to a size compatible with the foldi

241 t') that enable a relatively large region of conformational space to be searched.

242 reduced but still relevant subset of protein conformational space to improve computational efficiency

243 nfolded protein makes a Brownian walk in the conformational space to the folded structure, with each

244 Exploration of the side chain conformational space using molecular modeling approaches

245 zyme activity, we have determined the MBD1-3 conformational space using small angle X-ray scattering

246 ed by the TASSER methodology, which searches conformational space via parallel hyperbolic Monte Carlo

247 igh temperature, in which a greater range of conformational space was explored (4.3 angstroms RMS dev

248 The impact of substituent effects on the conformational space was investigated by Monte Carlo sim

249 Conformational space was searched systematically by vary

250 Conformational space was searched with Allinger's MM3 an

251 n order to explore exhaustively the feasible conformational space, we propose here an interval Branch

252 act of these two factors on the magnitude of conformational space, we systematically enumerated and c

253 Preferences toward certain regions of conformational space were both present and dependent upo

254 se residues can sample additional regions of conformational space where it is possible to further sta

255 ulty with a new parameterization of backbone conformational space, which represents all degrees of fr

256 onal states predominantly across a region of conformational space with bend angles between 24 and 85

257 nstrates the existence of a single region in conformational space with high propensity for Calpha-H..

258 sampling of protein backbone and side-chain conformational space with Rosetta can be leveraged to me

259 by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein d

260 For, the search of the conformational space with the use of the conformational

261 finement to physically reasonable regions of conformational space within the range of possibilities t