ライフサイエンスコーパス: secondary structure

1 d graph representations of RNAs from a given secondary structure.

2 ic and aggregated complexes with an unstable secondary structure.

3 sis supports the presence of a conserved RNA secondary structure.

4 which are excised from a stable hairpin-like secondary structure.

5 the conservation of the primary sequence and secondary structure.

6 tes and have a more pronounced impact on RNA secondary structure.

7 alterations were seen in lipids and protein secondary structure.

8 5.8S rDNA sequence to fold into a conserved secondary structure.

9 te RNA splicing, stability, translation, and secondary structure.

10 depicting the alignment of sequences on the secondary structure.

11 acid, to participate in an alpha-helix-like secondary structure.

12 can be stimulated by RNAs containing limited secondary structure.

13 single stranded region of the potential RNA secondary structure.

14 spectrum in methanol inferred a right-handed secondary structure.

15 eterogeneity and lack of persistent tertiary/secondary structure.

16 orm internal base pairs, leading to a folded secondary structure.

17 tional RNAs have an evolutionarily conserved secondary structure.

18 er, accompanied by a complete loss of native secondary structure.

19 of transfer RNAs, which exhibit a conserved secondary structure.

20 n, upstream open reading frames (uORFs), and secondary structure.

21 to allow the passage of polypeptides with a secondary structure.

22 e both the ligand binding site and the local secondary structure.

23 volution with implications for targeting and secondary structure.

24 rmation of a sequence-structure pair for RNA secondary structures.

25 eptides limits their ability to adopt stable secondary structures.

26 ormation from both the sequence identity and secondary structures.

27 ases, which use ATP hydrolysis to unwind RNA secondary structures.

28 he presence of cross-beta and polyproline II secondary structures.

29 n to favor nucleation of canonical beta-turn secondary structures.

30 cts on flgM mRNA stability or predicted mRNA secondary structures.

31 teins with beta-propeller and alpha-solenoid secondary structures.

32 d 3) comparison of pairwise and multiple RNA secondary structures.

33 alization of numerical representation of RNA secondary structure; 2) detection of single-point mutati

34 within the CTCF-binding region can form two secondary structures, a hairpin and a quadruplex.

35 both predicted to contain a distinctive RNA secondary structure abutting the miR159 binding site.

36 benchmark for assessing the accuracy of RNA secondary structure alignment methods.

37 oncert with prior knowledge of the canonical secondary structure, allow accurate inference of non-can

38 could potentially weaken the inhibitory RNA secondary structure, allow for more efficient translatio

39 DEAD-box RNA helicases (DBRHs) modulate RNA secondary structure, allowing RNA molecules to adopt the

40 Our genome-wide mRNA secondary structure analysis indicated that operonic mRN

41 To identify the AdV portal, we performed secondary structure analysis on a set of AdV proteins an

42 Here we report the first direct secondary-structure analysis of individual amyloid inter

43 hed with proline residues that regulate both secondary structure and aggregation propensity.

44 ence entropy, root mean square deviation and secondary structure and disorder prediction.

45 s significantly smaller influence of peptide secondary structure and interactions with counterions in

46 ular localization studies to investigate the secondary structure and membrane interacting capacity of

47 difficult to determine, and the link between secondary structure and RNA conformation is only beginni

48 The I1 state has native-like secondary structure and shows strong anilino-8-naphthale

49 The secondary structure and solvent accessible regions of on

50 pends largely on intron length together with secondary structure and splice site score.

51 by these fermentative aroma compounds on the secondary structure and stability of VVTL1, a Thaumatin-

52 e charge carrier mobility through changes in secondary structure and suggests that polymers with more

53 ed "on-target" complexes, each with a target secondary structure and target concentration, and a set

54 II, and fingerprint regions, indicating that secondary structure and tertiary contacts are influenced

55 nto classes based upon conserved primary and secondary structure and their cognate effector molecule.

56 Here, we examine influences of DNA secondary structure and twist on protein-protein interac

57 sing so-called "ideal" folds rich in regular secondary structures and almost devoid of loops and dest

58 We find that reconstruction using secondary structures and contacts can deliver accuracy h

59 this field, including further studies on the secondary structures and cost-effective synthesis of pol

60 The rise of peptides with secondary structures and functions would have been a key

61 eful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can cont

62 The secondary structures and melting points of the chimeric

63 DNA secondary structures and methylation are two well-known

64 se 3'SS are typically sequestered within RNA secondary structures and poorly accessible compared with

65 We show that A-to-I editing stabilizes RNA secondary structures and reduces the accessibility of AG

66 rate that axial ligand changes do not affect secondary structures and stability.

67 h-unlike normal-composition RNAs-do not form secondary structures and which act as essentially struct

68 ing specific functions to distinct predicted secondary structures and will facilitate antiviral targe

69 processes in vivo, probably by relaxing RNA secondary structures and/or RNA-protein interactions, an

70 a complex with CT, appear to disrupt the CT secondary structure, and block its interaction with the

71 more unfolded, but it retains some residual secondary structure, and shows weak anilino-8-naphthalen

72 detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and m

73 eristic 2D IR features of amyloid beta-sheet secondary structure are created by as few as four or fiv

74 involving both mechanical bonds and a folded secondary structure are one of the most promising archit

75 ering dynamics gated by transient changes in secondary structure are quite common in RNA.

76 Our findings suggest that secondary structures are invaluable companions of contac

77 e RNA primary sequences, while corresponding secondary structures are optional.

78 estimating the folding energy changes of RNA secondary structures are used in structure prediction an

79 foldamers, oligomers that adopt well-defined secondary structures, are now known, including many exhi

80 translation efficiency of mRNAs with strong secondary structures around the start codon is more depe

81 nge on predicted base-pair probabilities and secondary structures as compared to the standard paramet

82 ssimilarity, these RNA elements adopt common secondary structures (as revealed by 2D-1H NMR spectrosc

83 Secondary-structure assays revealed that monomers of bot

84 mino acid residues to participate in helical secondary structure at room temperature in the absence o

85 solubility, and the flexibility of proteins secondary structure at the pH studied.

86 mass spectrometric analysis to compare their secondary structures at near amino acid resolution.

87 ion problem, and RTEL1, which dismantles DNA secondary structures at telomeres to facilitate replisom

88 -40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary int

89 K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel be

90 RNA in terms of both nucleotide sequence and secondary structure but differs from it in that its regu

91 globule-like state where PepX maintained its secondary structure but the tertiary structure was subst

92 oth ions closely approach the surface of RNA secondary structure, but the completely folded RNA terti

93 Our procedure maintains RNA secondary structure by treating hydrogen bonds between b

94 DNA damage and secondary structures can stall the replication machinery

95 ensive rigid-body shifts as well as dramatic secondary structure changes.

96 sb binding, mainly imposed by biases in mRNA secondary structure, codon usage, and Ssb action.

97 molecules able to adopt well-defined stable secondary structures comparable to those found in nature

98 the propensity to dimerize and perturbs the secondary structure composition.

99 antibodies to the peptide and the beta-sheet secondary structure conformation.

100 The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation

101 chroism spectroscopy was used to confirm the secondary structure content and the stability through te

102 utilized for determining the percentages of secondary structure content present in proteins.

103 raldehyde until it reached a high beta-sheet secondary structure content, and species between 10-100k

104 mation of a protein; not only its percentage secondary structure content, but also the juxtaposition

105 ds significantly independent on family size, secondary structure content, contact range, or the numbe

106 ry properties of pre-mRNA, including the RNA secondary structure context.

107 The predictability of the foldamer secondary structure coupled to the high level of control

108 Therefore, it appears that this RNA secondary structure demarcates MYB33/65 as sensitive tar

109 Here, we report on the substrate secondary structure dependence of the PA channel.

110 This model of secondary structure-dependent selection of cryptic 3'SS

111 ., splicing, editing, and modification), RNA secondary structures, disease-associated variants, and g

112 G-quadruplexes (G4s), DNA secondary structures displaying noncanonical Watson-Cric

113 sually are unable to maintain their original secondary structures due to the lack of the restriction

114 he substitutions on peptide oligomerization, secondary structure dynamics, fibril assembly dynamics,

115 well-established technique for studying the secondary structures, dynamics, folding pathways, and in

116 A number of protein-inspired secondary structures (e.g., helices, sheets) have been p

117 NCX1 palmitoylation is governed by a distal secondary structure element rather than by local primary

118 modulate 3D structural rearrangements, while secondary structure elements guide large parts of the mo

119 The regular, repeating, chiral nature of secondary structure elements leads to intense bands in t

120 Analyses of secondary structure elements revealed substantial change

121 diated platelet adhesion and resolve dynamic secondary structure elements that regulate the binding p

122 e reflected in an increased dynamics of some secondary-structure elements in the capsid shell from wh

123 ity of side chains and their ability to form secondary structures, enable their broad applications in

124 four or five strands and so identify amyloid secondary structure even if the aggregates themselves ar

125 ighly ordered beta-sheets typical of amyloid secondary structure even if the fibers themselves are to

126 All 22 tRNA genes had typical cloverleaf secondary structures, except for trnS1 (AGN) which appea

127 sentation) of RNA sequence and corresponding secondary structure features are provided.

128 changed from neutral to acidic, whereas its secondary structure features remained nearly invariable.

129 on of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs.

130 to propose a mechanism whereby genomic ssDNA secondary structure formation during ssDNAp-to-target gD

131 e of the exit tunnel is to prevent excessive secondary structure formation that can interfere with th

132 y to protect it from degradation and prevent secondary structure formation.

133 cessary for transcription process stimulates secondary structure-formation thereby amplifying the pot

134 plexes (G4s) are extremely stable DNA or RNA secondary structures formed by sequences rich in guanine

135 i-Motifs are alternative DNA secondary structures formed in cytosine-rich sequences.

136 can be created via limited DNA synthesis at secondary-structure forming sequences.

137 hypersensitive site with three potential DNA secondary structure-forming regions.

138 The K2hPg/VKK38 binding altered the VKK38 secondary structure from a helical apo-peptide with a fl

139 that integrates sequentially building ssDNA secondary structure from sequence, constructing equivale

140 edge weights in graphs reflecting different secondary structures further improves the accuracy.

141 identified the in vitro presence of a stable secondary structure, G-quadruplex (G4) in the 5' UTR of

142 these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich stran

143 in some cases leading to formation of other secondary structures (hairpin-->duplex).

144 l complexes that can specifically target DNA secondary structure has attracted considerable attention

145 Algorithmic prediction of RNA secondary structure has been an area of active inquiry s

146 at a region of viral RNA devoid of extensive secondary structure has IRES activity and produces low l

147 these micellar aptamers retain their native secondary structure in a crowded environment and are sta

148 Collectively, 5 induces strong secondary structure in Abeta and inhibits its functions

149 ize a model CPP-penetratin-and determine its secondary structure in different cellular compartments.

150 ly identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei.

151 peptide termini and the influence of peptide secondary structure in HILIC.

152 dely accepted, yet the contribution of their secondary structure in mineral formation remains to be c

153 elling evidence for the role of a disordered secondary structure in phosphoproteins in bone-like apat

154 x RNA-dependent ATPase thought to unwind RNA secondary structure in the 5'-untranslated regions (UTRs

155 DNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions.

156 aS acquires an alpha-helical secondary structure in the presence of DHA and, in turn,

157 Induction of secondary structure in the silk constructs was confirmed

158 Secondary structure in the tetrameric apoE3 and E4 isofo

159 itting, unravels three distinct pH-dependent secondary structures in phosvitin.

160 w that splicing yields distinct local 5'-UTR secondary structures in SERPINA1 transcripts.

161 ies show that compound 1 also forms extended secondary structures in solution.

162 lve interactions between capsid proteins and secondary structures in the viral genome, as exemplified

163 uction accuracy using true contacts - adding secondary structures, increasing contact distance thresh

164 e form of an RNA:DNA hybrid segment or bulky secondary structures, indicating a dsRNA scanning mode o

165 cation of transcription termination, how RNA secondary structures influence this process and whether

166 el method (RS3D) that can assimilate the RNA secondary structure information, small-angle X-ray scatt

167 veloped, including nanoparticle carriers and secondary structure interference inhibitor systems.

168 ucture components by abstracting the overall secondary structure into smaller substructures composed

169 nd simple approach to identify predicted RNA secondary structures involved in genome packaging in the

170 beta-Sheet secondary structure is a common feature of amyloids, but

171 ensation, suggesting that disulfide-mediated secondary structure is also critical for proper protamin

172 The TR secondary structure is believed to play a role in CAG ex

173 earliest events in unfolding, 3.5 ms before secondary structure is disrupted.

174 In addition to these linear motifs, RNA secondary structure is emerging as an important layer in

175 M, but highly ordered beta-sheets of amyloid secondary structure is identified from the 2D IR spectra

176 However, although a large contributor, secondary structure is not the only factor that influenc

177 length show that polyU, despite its lack of secondary structure, is packaged more efficiently than v

178 re predisposed to fold into specific ordered secondary structures, is of significant interest.

179 on of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating

180 ay activation reactions in general, that RNA secondary structure may be important to its procoagulant

181 e sodium/calcium exchanger now suggests that secondary structure may hold the key to understanding th

182 Thus, lncRNA secondary structure may regulate IL-1alpha expression.

183 ing of hydrophobic proteins and folding into secondary structures mediated by Ca(2+) and Mg(2+) toget

184 oligonucleotides were designed based on the secondary structure model and tested against influenza v

185 a number of nucleic acid, thermodynamic and secondary structure models on real CRISPR datasets.

186 uanine quadruplex (G4) structure in DNA is a secondary structure motif that plays important roles in

187 We find an increase in secondary structure motifs at longer Q-lengths, includin

188 By focusing on secondary structure motifs composed of specific two base

189 ilus S15 can either recognize many different secondary structure motifs or some aspects of the intera

190 We found a group of purine-uracil repeat RNA secondary structure motifs plus other motifs in neuron r

191 s can be used to classify five canonical RNA secondary structure motifs through principal component a

192 e-specific classification of two independent secondary structure motifs.

193 en telechelic polymers that feature distinct secondary structure motifs.

194 side differentially expressed mRNAs with RNA secondary structure motifs.

195 e for thioglycine in stabilizing the protein secondary structure near the active site.

196 ed in cells than in vitro and have predicted secondary structures no more stable than those of random

197 Third, although the secondary structures observed in CHARMM36 and CHARMM22/c

198 The unusual secondary structure of 1 was confirmed by spectroscopic

199 e ability to both localize and determine the secondary structure of a CPP within cells is critical fo

200 However, this secondary structure of chromatin remains poorly understo

201 By stabilizing the secondary structure of chromatin, we confirmed a nucleos

202 l polysaccharides induced similar changes in secondary structure of gluten proteins concerning format

203 The secondary structure of HZ was characterized, and it was

204 Ultrasonication altered the secondary structure of kafirin as evaluated by circular

205 This requires precise knowledge of the secondary structure of new compounds and the ability to

206 ns between OprH and LPS mainly depend on the secondary structure of OprH and the chemical structure o

207 ed to specifically react with the beta-sheet secondary structure of pathological oligomeric conformer

208 tructure analysis showed that the determined secondary structure of segment 5 (+)RNA is mostly conser

209 e sites for oligonucleotides in the revealed secondary structure of segment 5 (+)RNA.

210 d formation mechanism and the quaternary and secondary structure of soluble NFGAIL oligomers.

211 tion, results in a significant change in the secondary structure of the corresponding oligomers.

212 ry (HDX-MS) we show that Ric-8A disrupts the secondary structure of the Galpha Ras-like domain that g

213 re, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA.

214 scopic techniques, we were able to probe the secondary structure of the materials and verify the pres

215 variate data analysis to quantify changes in secondary structure of the multifunctional calcium-bindi

216 ) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele f

217 e sort of structural polymorphism, where the secondary structure of the peptide is altered strongly b

218 ism spectroscopy was used to investigate the secondary structure of the peptide upon binding with eit

219 se 11 amino acids neither alters the overall secondary structure of the protein, nor affects its stab

220 These findings illustrate that the secondary structure of the RNA molecule-and its absence-

221 ality depends on segment length, the type of secondary structure of the segment and local quality of

222 The secondary structure of wine VVTL1 was not strongly affec

223 The conserved sequence and distinct secondary structures of kink-turns (k-turn) suggest comp

224 ing sites which can significantly impact the secondary structures of lncRNAs and lncRNA-miRNA interac

225 atistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR,

226 odulation of the translocation efficiency by secondary structures of the nascent peptide chain, we pe

227 generate peptide nanofibers with predefined secondary structures of the peptides by a rational desig

228 Predicted secondary structures of these regions revealed stem-loop

229 strate concurrent targeting of different DNA secondary structures offers an effective, precise, medic

230 ng conditions and in the absence of residual secondary structure, OmpLA populates an ensemble of slow

231 igation of the fine-scale effects of peptide secondary structure on peptide mobility.

232 ), to reveal the effect of different protein secondary structures on hydration water.

233 impact of transcription factors (TF) and RNA secondary structures on the regulation of gene expressio

234 stored by putative t2M/t4M refolding of stem secondary structure or tertiary bridging interactions be

235 oding oligo-U domains as potential sites for secondary structure or tertiary contact.

236 e mutations do not induce changes in protein secondary structures, or shared effects on oligomerizati

237 single-stranded configuration, showing that secondary structure plays a key role in these processes.

238 A sequence and a predicted alteration of its secondary structure, potentially explaining a subsequent

239 Protein secondary structure prediction (SSP) has been an area of

240 An RNA folding/RNA secondary structure prediction algorithm determines the

241 s of 512 bacterial Tat signal peptides using secondary structure prediction and docking algorithms su

242 The workhorses of the RNA secondary structure prediction engine are recursions fir

243 Secondary structure prediction identified three disorder

244 Secondary structure prediction is an important problem i

245 Understanding how RNA secondary structure prediction methods depend on the und

246 comparative sequence analysis algorithm for secondary structure prediction of multiple homologs, whe

247 ters were derived for use in free energy and secondary structure prediction software.

248 the benefit of experimental mapping data in secondary structure prediction to homologous sequences.

249 protein residue-residue contact prediction, secondary structure prediction, and fold recognition.

250 e the parameters with the greatest impact on secondary structure prediction, and the subset which sho

251 synthetic theophylline riboswitches based on secondary structure prediction.

252 ds to provide structural constraints for RNA secondary structure prediction.

253 ermodynamic energy minimization were used in secondary structure prediction.

254 Secondary structure predictions as well as mature miRNA

255 We also provide in silico and in vivo secondary structure predictions for comparison, visualiz

256 s backbone and sidechain dynamics as well as secondary structure propensities as features.

257 ervation between fibrils revealed invariable secondary-structure properties, however, with inter-mono

258 ecursors (oligomers) long enough to ensure a secondary structure, rather than from polymerization pro

259 e majority of functional RNAs show conserved secondary structures, rather than sequence conservation.

260 5' end of the viral genome involving an RNA secondary structure required for RNA replication have be

261 portions of 5' stem-loop I, which is an RNA secondary structure required for viral RNA replication.

262 ely to disrupt the correct folding of an RNA secondary structure required for viral RNA replication.

263 tospacer-flanking sequence and elucidate RNA secondary structure requirements for targeting.

264 Investigations of the underlying aptamer secondary structure revealed differences between in sili

265 energy calculations of stochastic samples of secondary structures revealed a correlation between para

266 ll-length zorO 5 UTR folds into an extensive secondary structure sequestering the ribosome binding si

267 nanocomposite film have been changed in its secondary structure so that it provided an enzyme like a

268 the features analysed by JoY, which include secondary structure, solvent accessibility and sidechain

269 xt-generation sequencing is transforming RNA secondary structure studies in living cells.

270 that participate in the formation of various secondary structures such as G-quadruplexes.

271 lly designed protein with a subtle and rigid secondary structure that enables the binding of substrat

272 ripts remain chromatin-associated and have a secondary structure that favors RNA:DNA hybrid formation

273 Viral IRES, in general, contain extensive secondary structure that is critical for activity.

274 n discrete functional regions with a defined secondary structure that regulate diverse biological pro

275 provide a novel mode of PC4 binding to a DNA secondary structure that remains within the framework of

276 nic mRNAs are comprised of ORF-wide units of secondary structure that vary across ORF boundaries such

277 of peptoid foldamers yields a new and unique secondary structure that we term an "eta-helix" due to i

278 science has motivated the development of new secondary structures that can serve as architectural ele

279 Frameshifting is induced by mRNA secondary structures that compromise ribosome fidelity d

280 that conserved synonymous sites and/or local secondary structures that might play a role in determini

281 ameters that describe the MSA, the predicted secondary structure, the predicted solvent accessibility

282 ubstitution arrangements impact the backbone secondary structure through different nonbonding F...H i

283 onal diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble.

284 Targeting DNA secondary structures thus represents a potentially new a

285 These non-swapped oligomers are identical in secondary structure to CysC monomers and completely reta

286 alpha-carbon or phosphate backbones through secondary structure to domains, molecules, and multimers

287 TurboFold II algorithm for prediction of RNA secondary structures to utilize basepairing probabilitie

288 d stabilization of G-quadruplex nucleic acid secondary structures triggers local epigenetic plasticit

289 ntary nucleic acids that break the aptamers' secondary structure upon hybridization.

290 uences alone, the web server can compute the secondary structures using free energy minimization algo

291 s strategy allows a remarkable change of the secondary structure via a small modification.

292 iblock copolymer scaffolds featuring diverse secondary structures via the directional assembly of tel

293 ames for predicting protein tertiary and RNA secondary structures, we have developed an open software

294 Protein specificity and secondary structure were confirmed by Western Blot and C

295 pped the TP functions according to predicted secondary structure, where it folds into alpha helices o

296 The control over their secondary structures, which enables dynamic conformation

297 nize into pentagonal and hexagonal prismatic secondary structures, which then form tetrahedral and di

298 oth rational and modular control of foldamer secondary structure, while maintaining the capacity for

299 logical conditions reveals that a disordered secondary structure with a low content of PII helix is r

300 the hybrid sequence, which should alter the secondary structure without compromising the immunogenic