ライフサイエンスコーパス: threading

1 nd reduced computation time through multiple threading.

2 nces, conversion of FASTQ formats, and multi-threading.

3 iously proposed consecutive-hopping model of threading.

4 sulting in a negative activation enthalpy of threading.

5 e 3D structure could be predicted by protein threading.

6 ocessing time as a result of increased multi-threading.

7 nique dimeric toroidal configuration for DNA-threading.

8 ll lead to improvement of the performance of threading.

9 nt scoring function for low-homology protein threading.

10 considered to be less accurate than that by threading.

11 omains that were determined by computational threading.

12 AST is implemented in C++ and supports multi-threading.

13 ing time, the code uses clustering and multi-threading.

14 e domain is required for DNA binding but not threading.

15 ion to occur or to allow through-the-annulus threading?

16 own knotted protein topologies: knotting via threading a native-like loop in a preordered intermediat

17 ch as pantomimes that signify actions (e.g., threading a needle) or emblems that facilitate social tr

18 he kinetic and thermodynamic consequences of threading a polypeptide chain.

19 ional (3D) models of dimers are generated by threading a target amino acid sequence through several s

20 We present "molecular threading", a surface independent tip-based method for s

21 er target are 0.266, 0.336, and 0.362 by the threading algorithm SP(3), original TASSER and chunk-TAS

22 Depending on the threading algorithm used, it yields on average 4-16% hig

23 This paper presents a new genomic threading algorithm which integrates the gene finding an

24 onsensus restraints generated by an improved threading algorithm, PROSPECTOR_3.5, which uses computat

25 4, and a new local structural fragment-based threading algorithm, STITCH, implemented in two variants

26 The development of improved threading algorithms for remote homology modeling is a c

27 first recognized from the PDB using multiple threading alignment approaches.

28 in 3D structure modeling, combining multiple threading alignment information should increase the accu

29 In the case of threading, alignment accuracy strongly influences the fr

30 dimensional (3D) atomic models from multiple threading alignments and iterative structural assembly s

31 which ensure the quick generation of initial threading alignments compared with traditional remote-se

32 to combine the ab initio model with multiple threading alignments for further improving the robustnes

33 mportantly, the quality of the corresponding threading alignments is comparable to these constructed

34 nition accuracy was observed when inaccurate threading alignments were used to identify common residu

35 domain boundary locations based on multiple threading alignments.

36 maps, are automatically constructed from the threading alignments.

37 etermined by the magnetic flux quantum, h/e, threading an area defined by the atomic interlayer separ

38 l is similar to one derived previously using threading analysis, a distinct computational approach, s

39 ces in recent decades on sequence alignment, threading and alignment-free methods, protein homology d

40 udies revealed that the rates of the polymer threading and dethreading in and out of the dimeric syst

41 mpatible with these commonly used in protein threading and fold recognition.

42 Comparative modeling by threading and homology modeling of the NTPDase3 sequence

43 ein modeling (TM) methods, including protein threading and homology modeling, especially when the seq

44 eling process, including sequence alignment, threading and loop building.

45 s assembled in a suspended lipid membrane by threading and mechanically capturing a single strand of

46 The alpha-helical structure, as modeled by threading and molecular dynamics simulations, tends to f

47 theoretical speed-up in comparison to multi-threading and MPI techniques.

48 gateway formed by two helices enforces ssDNA threading and specificity for free 5' ends.

49 Moreover, multi-threading and support to Sun Grid Engine (SGE) are imple

50 ng that [PSI(+)] propagation depends on this threading and that Hsp104 "breaks" prion aggregates by e

51 Kinetic investigations of the threading and translation of the double helix along mult

52 ed modeling (including homology modeling and threading) and free modeling.

53 onstructed using chemical cross-linking, MS, threading, and ab initio approaches.

54 n comparative modeling, fold recognition and threading, and first-principles techniques.

55 escape has stronger voltage dependence than threading, and that threading is sensitive to polymer or

56 ix adopts a hairpin-like configuration while threading, and the minor route to an entropically limite

57 model significantly outperforms the standard threading approach in binding energy prediction.

58 Motivated by the ability of a simple threading approach to predict MHC I--peptide binding, we

59 We introduce a threading approach, iWRAP, which focuses only on the pro

60 ide complexes that were used in the original threading approach, we included three other sources of i

61 the integration of the deep profiles and new threading approaches into LOMETS2 significantly improve

62 eading programs, including contact-map-based threading approaches, (ii) deep sequence search-based se

63 ts towards the development of more sensitive threading approaches, confident structural models cannot

64 variable regions lead to vague alignments in threading approaches.

65 overlapping scheme, multithreading and hyper-threading, are exploited to improve the execution perfor

66 The iterative threading assembly refinement (I-TASSER) server is an in

67 , 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, wh

68 tein structure prediction algorithm, pro-sp3-Threading/ASSEmbly/Refinement (TASSER), is described and

69 %) higher than the best machine learning (or threading)-based method.

70 Furthermore, the threading-based and docking methods were better than the

71 The centerpiece of the pipeline is our threading-based program PROSPECT.

72 ms and addressed the fold stability issue of threading-based structure prediction by molecular dynami

73 r organisation with nanoscale water channels threading between macromolecular regions within a dynami

74 RT and NiPRT, respectively) were achieved by threading bis(azide)bis(amide)-2,2'-bipyridine axle into

75 uence-specific interaction of DNA with a new threading bisintercalator (C1) consisting of two interca

76 G2000 chains is only three times slower than threading by a conjugate with triethylene glycol chains

77 For example, macrocycle threading by a dye conjugate with two appended PEG2000 c

78 lity of contact information to boost protein threading by developing a new contact-assisted threading

79 ecting from several structural templates for threading calculations and adding random sequences to th

80 e, over the endo-benzyl one, was observed by threading calix[8]-wheel 3 with the directional n-butylb

81 Furthermore, partial N-terminal threading can play a role in self-association, whereas w

82 It is written in C/C++, includes multi-threading capabilities, and is compatible with the BAM f

83 nalysis pipeline (R-SAP) with built-in multi-threading capability to analyze and quantitate high-thro

84 interactions between the positively charged threading component and macrocyclic ligand, together wit

85 between the anion template and the cationic threading component, and to a lesser extent favorable se

86 imidazolium, benzimidazolium and guanidinium threading components, and macrocyclic isophthalamide pol

87 ormance for a template-based method based on threading (COTH) and another template-based method based

88 neous compositional and strain profiles, low threading defect densities, and atomically planar surfac

89 Molecular threading demonstrates high straightness and uniformity

90 The rate of DNA threading depends exponentially on force, consistent wit

91 cular dendronized polymers, as well as their threading-dethreading properties, were characterized by

92 ly asymmetric dumbbell, which can impair the threading/dethreading of a [2]pseudorotaxane, and (ii) c

93 The threading dislocation densities estimated by plan-view t

94 neous compositional and strain profiles, low threading dislocation densities, and atomically planar s

95 e, and pure GaN layers on Si with the lowest threading dislocation density of 1.1 x 10(7) cm(-2) achi

96 the onset and progression of diffusion along threading dislocations in sequentially annealed nitride

97 lysis of peak widths, it was determined that threading dislocations in the top 6 microns of the wafer

98 Additionally, the density of threading dislocations in these region is one order of m

99 posure of CO to active sites (step edges and threading dislocations) on a Au(111) surface.

100 plate with high crystal quality and very few threading dislocations, allowing for further re-growth o

101 factory model that retains the advantages of threading DNA through colocalized replisomes at about eq

102 R characteristics, including hydrophobicity, threading efficiency and surface charge, were found to b

103 suppression of the translocation through the threading-entanglement with the linear matrix chains.

104 Here, we provide direct evidence that a threading event associated with formation of either a 31

105 Previous studies indicated that the threading event that creates the 52 knot occurs during t

106 th 72.7% precision on the proteins for which threading failed to detect any DCDs.

107 alated between the base pairs of ct-DNA in a threading fashion, however, exhibits emission maximum at

108 tructure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with

109 volves template identification by multimeric threading, followed by multimer model assembly and refin

110 The facile synthesis utilizing a "threading-followed-by-clipping" protocol features Cu(2+)

111 or-acceptor template-directed syntheses in a threading-followed-by-cyclization protocol employing Cu(

112 d by donor-acceptor templation, employing a "threading-followed-by-cyclization" approach.

113 ructural models by the iterative assembly of threading fragments.

114 Overhauser effect spectroscopy--to adopt the threading geometry.

115 at were created during insertion of the self-threading implants, subsequent to repeated MTD measureme

116 lution evaluation methods are based on multi-threading implementation on a single computer with very

117 olved ColE9's unstructured N-terminal domain threading in opposite directions through two OmpF subuni

118 We also implemented multi-threading in RAPSearch2, and the multi-thread modes achi

119 Values of Ka and kon for macrocycle threading in water are reported for a series of homologo

120 ext-specific alignment potential for protein threading, including alignment and template selection.

121 Serial puncture and linear threading injection styles had similar transfer incidenc

122 erived structures for these complexes show a threading intercalation binding mode with slow and chira

123 We investigated DNA threading intercalation by binuclear ruthenium complex [

124 the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthen

125 the emission enhancement did not arise from threading intercalation of the complex.

126 easure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA i

127 talytic oxidation of ascorbic acid (AA) by a threading intercalator (N,N'-bis(3-propylimidazole)-1,4,

128 Dumbbell-shaped DNA threading intercalators represent the next order of stru

129 Our data suggest that mRNA threading into the ES6S region makes scanning by 48S PIC

130 After threading into the SecYEG translocon, transmembrane segm

131 DNA intercalation by threading is expected to yield high affinity and slow di

132 Threading is interrupted by pauses that are found to be

133 he design of an apparatus used for molecular threading is presented, and fluorescence and electron mi

134 voltage dependence than threading, and that threading is sensitive to polymer orientation while esca

135 ex and that the free energy barrier to chain threading is significantly lower than the hydrolysis bar

136 nce and structure levels and have shown that threading is, in general, a viable approach for modeling

137 mologous template structures identified from threading, is described.

138 ing, including homology modeling and protein threading, is the most reliable method for protein 3D st

139 rotaxane complexes as well as to a favorable threading kinetic.

140 Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed

141 squaraine core that ensures fast macrocycle threading kinetics, and (c) sialic acid blocking groups

142 By structurally threading low-resolution structural models through the B

143 n outline of known mechanistic principles of threading machines that unfold protein substrates either

144 Many other AAA+ proteins function by threading macromolecules through a central pore of a dis

145 Hence, models involving TerS-mediated DNA threading may be excluded as an essential mechanism for

146 molecular basis to inhibition through a DNA "threading" mechanism.

147 We developed LOMETS, a local threading meta-server, for quick and automated predictio

148 Experimental results indicate that our threading method greatly outperforms the best profile-ba

149 Tested on the CASP8 hard targets, our threading method is also better than all the top CASP8 s

150 ploying our newly-developed contact-assisted threading method over a large-scale benchmark dataset us

151 structure of AatA was also predicted by the threading method using the I-TASSER online server and th

152 method is a classical single-template-based threading method without any post-threading refinement.

153 vement as compared with RAPTOR (a well-known threading method) and even a mean 18% (median 10%) impro

154 We present a novel protein threading method, CNFpred, which achieves much more accu

155 reading by developing a new contact-assisted threading method.

156 ficantly more efficient than the "final-step-threading" method employed previously and enables the sy

157 Threading methods extend coverage further into the twili

158 ed as a template database in the homology or threading methods for modeling the 3D structures of unkn

159 gnments should enhance homology modeling and threading methods for predicting PPIs by providing a bas

160 r alignments than the best profile-based and threading methods on several public (but small) benchmar

161 ctions derived from the previously developed threading methods PROSPECTOR_3 and SP(3).

162 as observed for beta-class proteins when the threading methods were used because the average alignmen

163 ections in the development of more sensitive threading methods with the enhanced capabilities of targ

164 t state-of-the-art profile- or contact-based threading methods, respectively, for the Hard targets th

165 ily, than the best profile- or contact-based threading methods.

166 ld strength required to drive transport, the threading mobility, and the transport mobility were meas

167 tive double threading, the parameters of the threading model are learnable, and both MHC and peptide

168 We propose a threading model for movement of DNA loops around the per

169 To train this CNF threading model, we employ a novel quality-sensitive met

170 e P22 portal ring complexes and validate the threading model, we performed comparative hydrogen/deute

171 vement regarding structural details over the threading model.

172 o the C-terminal domain, consistent with our threading model.

173 or soluble substrates, indicating a "partial threading" model of translocation.

174 Hypothetical ring-ring stacking and peptide threading models for Rubisco reactivation are briefly di

175 ular knots focus on twisting, folding and/or threading molecular building blocks.

176 s increased, or the protonation state of the threading mono-terephthalate anion is changed.

177 h the use of homology modeling and structure threading, NDR1 was predicted to have a high degree of s

178 Most of the systems are found to display a threading network which percolates the system.

179 Apparently, interactions related to threading occur only when the flap is greater than two t

180 Laser-induced threading occurs on a large scale in water, tracked via

181 Thus, it was found that such threading occurs only upon partial preorganization of th

182 ervers in a high-acuity visuomotor task, the threading of a needle in a computer-simulated virtual en

183 s at high helicase concentrations, occurs by threading of a preassembled helicase over free 5'-ends,

184 bonyl groups of the CB7 molecules avoids the threading of a second CB7 molecule yielding a mixed stru

185 We describe here the mechanism of threading of a series of polymers through a flexible mac

186 elies on Hsp70 function and on ATP-dependent threading of aggregated polypeptides through the pore of

187 Through-the-annulus threading of calix[5]arene penta-O-ethers by dialkylammo

188 In this system, threading of CB[7] on the particle surface reduces the c

189 The threading of conformationally stable 1,2,3-alternate cal

190 d observations are discussed in terms of the threading of DNA through T-ag hexamers and the initiatio

191 Threading of DNA through the central channel of a replic

192 nano-assembly through plasmon-induced laser threading of gold nanoparticle strings, producing conduc

193 mational fluctuations arise due to transient threading of linear polymers through open ring chains st

194 The threading of monostoppered alkylbenzylammonium axles 7(+

195 are orientationally biased and result in the threading of over 60 amino acids through 2 subunits of O

196 The threading of pentapeptides into the beta-helical fold is

197 Homology threading of prokaryotic transporters based on the X-ray

198 feature of this stability is the topological threading of RNA through the complex and/or around the D

199 NA-protein interactions using voltage-driven threading of single DNA molecules through a protein nano

200 Clp ATPases is based on an energy-dependent threading of substrates through the narrow pore at the c

201 ation in a step that may involve facilitated threading of the 5' ssDNA flap.

202 ructural analysis of CuPRT revealed complete threading of the axle fragment into the wheel cavity, wh

203 The threading of the calix[5]arene wheels with the asymmetri

204 limiting step which is likely to involve the threading of the chain to form the 52-knot occurs late o

205 translocation, force unfolding, and mediate threading of the denatured protein through the ClpX pore

206 eric hindrance of the axle phenyl group, the threading of the guest was seen to occur in a unidirecti

207 ficity for KDM2A is mediated by the U-shaped threading of the H3K36 peptide through a catalytic groov

208 A complete study of the through-the-annulus threading of the larger calix[8]arene macrocycle with di

209 he knotted proteins clearly demonstrate that threading of the nascent chain through a knotting loop o

210 utotransporter secretion is C --> N-terminal threading of the passenger domain through the outer memb

211 bacterial and the algal systems and involves threading of the rubisco large subunit C terminus.

212 nent blockade of ionic current is due to the threading of the tether through the channel.

213 vity, in combination with the face-selective threading of viologen-type axles afforded by tris(N-phen

214 ence-to-structure alignments (also known as 'threading') of membrane proteins using the FUGUE alignme

215 cooperative action, for example by multiple threading on a single polysaccharide molecule.

216 kflow system accelerated with MPI and Python threading on compute clusters.

217 ure prediction of P22 portal protein and its threading onto the crystal structure of the Phi29 portal

218 scoring criterion to identify sequences and threadings optimally suited to the LHBH, as in a fold re

219 volutionary related proteins (as detected by threading or functional analyses) are excluded.

220 dyes are large enough to prevent macrocycle threading or rotaxane unthreading.

221 cognition and binding of the flap base, then threading over the 5'-end of the flap, and cleaving peri

222 We re-evaluated multiple options, such as threading, parallel garbage collection, I/O options and

223 Users can also use the advance and multiple threading parameters for complex metabolic modeling.

224 ted into the dimer by a mechanism we termed "threading," passing between parts of the preassembled be

225 rther found that Hsp104 mutants defective in threading peptides through the hexamer pore had reduced

226 ontacts and its possible utility in boosting threading performance for improving low-homology protein

227 orrelation Coefficient (MCC) >= 0.5 improves threading performance in nearly 30% cases, while low-qua

228 sults serve to illustrate the versatility of threading polyintercalation given that, in a previous st

229 this study involves the use of rapid protein threading predictor (RAPTOR) to generate tertiary struct

230 Interestingly, by (1)H NMR monitoring of the threading process between 8(+) and 3, we revealed two ca

231 iar NMR features are here evidenced for this threading process involving the less symmetrical 1,2,3-a

232 roscopy were used to provide evidence of the threading processes.

233 interface, we utilized the Phyre structural threading program and found that ImaA has a region with

234 Nine state-of-the-art threading programs are installed and run in a local comp

235 Next, multiple threading programs are performed for homologous structur

236 lopments, including (i) new state-of-the-art threading programs, including contact-map-based threadin

237 er finding also being supported by iterative threading protein modeling.

238 emperature-dependent studies reveal that the threading rate increases on decreasing the temperature,

239 The threading rate is hardly affected by the length of the P

240 late-based threading method without any post-threading refinement.

241 her select the geometry and stiffness of the threading region of the newly fused protein.

242 impacts the performance of contact-assisted threading remains elusive.

243 dings, we then proceeded to demonstrate that threading represents a useful tool for structure predict

244 The threading requirement prevents this active nuclease from

245 lying that short flaps are cleaved without a threading requirement.

246 SP threading requires smaller forces when the SP is pulled

247 enerates significantly better alignments and threading results than the best profile-based methods on

248 In addition, by employing multi-threading, rMAPS2 has vastly improved the user experienc

249 ed from the top predictions of the component-threading servers, which are at least 7% more accurate t

250 e for the OBD central channel in binding and threading ssDNA during unwinding of circular SV40 DNA.

251 ffects on the barrier for the intramolecular threading step has been examined with the result that th

252 , coupling the energy from ATP hydrolysis to threading substrate proteins (SP) through their narrow c

253 ter is written in C++ using OpenMP for multi-threading support.

254 nstrated in rotaxane shuttles and macrocycle threading systems, the sensitivity of speed bump effects

255 roadly applicable to many types of molecular threading systems.

256 ome searching of conformational space as the threading takes place.

257 utative new chemokine was the application of threading techniques to its uncharacterized sequence.

258 ls and the conservation scores from multiple-threading template alignments.

259 tacts in proteins can be predicted from both threading templates and sequence-based machine learning.

260 tructure chunks of a given target as well as threading templates for obtaining contact potentials and

261 the consensus significance score of multiple threading templates is introduced to estimate the accura

262 consensus contact predictions from multiple threading templates.

263 estraints derived from the chunks as well as threading templates.

264 36% more targets compared to using the best threading templates.

265 e we describe the DNA-binding behaviour of a threading tetra-intercalator.

266 We recently reported a threading tetraintercalator with a dissociation half-lif

267 Ku loads at a break by threading the DNA ends through a circular channel in its

268 er, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

269 o nucleosome-associated ends still occurs by threading the end through its channel, but rather than d

270 r is stabilized in part by the difficulty of threading the glycosylated end of the alpha-subunit loop

271 The second model was generated by threading the integrin's sequence onto TM helix dimers p

272 the amino acid or peptide guest molecules by threading the lysine or arginine side chain through the

273 Threading the NTD onto the AraC backbone revealed an alp

274 alternative strategy: stabilization through threading the sp-hybridized carbon chain through a phena

275 ins of similar folds and functional sites by threading the target structure through three representat

276 our approach, which we call adaptive double threading, the parameters of the threading model are lea

277 ls having been proposed: the "hairpin," the "threading," the "multimeric," and the "Omp85 (YaeT)" mod

278 n the upper surface of the AAA-1 ring before threading them through the ClpB hexamer in an ATP hydrol

279 ones exert ATP-fueled substrate unfolding by threading through a central pore.

280 SP threading through a nonallosteric ClpY nanopore involves

281 e to unfold diverse substrates by processive threading through its central pore.

282 uctural basis for N- to C-terminal substrate threading through the central cavity, enabling a clockwi

283 d TerS rings inspired models that invoke DNA threading through the central channel.

284 mmetry-related manner, with the alkyl linker threading through the minor grooves.

285 ore likely to follow the voltage gradient by threading through the narrowest constriction and translo

286 to correctly capture the time regime of mRNA threading through the pore and subsequent transport.

287 We present a model of DNA threading through the T-ag complex illustrating how sing

288 ange slowly, whereas flexible connector Nups threading throughout the NPC architecture exchange more

289 nzymes employ a two-step mechanism for chain threading to form a Michaelis complex and that the free

290 base pair must be transiently melted for DNA threading to occur.

291 However, the existing threading tools perform poorly on remote homologous prot

292 acid blocking groups that prevent macrocycle threading until they are removed by viral neuraminidase.

293 his holds true even in CASP13 dataset, where threading using high-quality contacts (MCC >= 0.5) signi

294 al results demonstrate that contact-assisted threading using high-quality contacts having the Matthew

295 mal structures that are generated in gapless threading we show that the SPs and experimentally determ

296 dicting secondary structure by using gapless threading, which we advocate as an alternative method fo

297 o-OH functions give rise to a less efficient threading with respect to the endo-OR ones, in line with

298 amantyl groups give rise to a more efficient threading with respect to the exo-tert-butyl ones, leadi

299 acroring cannot give the through-the-annulus threading with them because of its small dimension.

300 ed how many pegs placed in 30 seconds), bead threading (with two sizes of bead, to increase the diffi