ライフサイエンスコーパス: threading

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

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

3 ll lead to improvement of the performance of threading.

4 nt scoring function for low-homology protein threading.

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

6 considered to be less accurate than that by threading.

7 omains that were determined by computational threading.

8 stabilizes the small seatbelt loop prior to threading.

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

10 nd reduced computation time through multiple threading.

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

12 iously proposed consecutive-hopping model of threading.

13 sulting in a negative activation enthalpy of threading.

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

15 are engineered at a supramolecular level by threading a conjugated macromolecule, such as poly(para-

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

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

20 A potential DNA-threading agent was designed by attaching different amin

21 MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein-protei

22 n 927 cases, the templates identified by our threading algorithm PROSPECTOR_3 have a rms deviation fr

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

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

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

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

27 4, and a new local structural fragment-based threading algorithm, STITCH, implemented in two variants

28 utational methods, including helixhunter and threading algorithms.

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

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

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

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

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

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

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

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

37 domain boundary locations based on multiple threading alignments.

38 maps, are automatically constructed from the threading alignments.

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

40 Threading analysis, which examines aspects of secondary

41 s of the major facilitator superfamily using threading analysis.

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

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

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

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

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

47 s residues, and a method of fold recognition/threading and homology modeling, we have computed a thre

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

66 variable regions lead to vague alignments in threading approaches.

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

68 , 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, wh

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

70 d side-chain based potential consistent with threading based tertiary restraints.

71 nd analysis, such as in a recently developed threading-based algorithm, MULTIPROSPECTOR.

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

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

74 The centerpiece of the pipeline is our threading-based protein structure prediction system PROS

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

76 ha) and side-chain-based potential driven by threading-based, predicted tertiary restraints.

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

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

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

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

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

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

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

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

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

86 request fold recognition by prediction-based threading, CHOP domain assignments, predictions of trans

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

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

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

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

91 Currently, the Genomic Threading Database (GTD) contains structural assignments

92 The Genomic Threading Database currently contains structural annotat

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

94 Molecular threading demonstrates high straightness and uniformity

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

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

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

98 The threading dislocation densities estimated by plan-view t

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

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

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

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

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

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

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

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

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

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

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

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

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

112 rvers in the areas of comparative modelling, threading/fold recognition, secondary structure predicti

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

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

115 that consists of template identification by threading, followed by tertiary structure assembly via t

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

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

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

119 ructural models by the iterative assembly of threading fragments.

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

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

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

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

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

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

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

127 We investigated DNA threading intercalation by binuclear ruthenium complex [

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

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

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

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

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

133 lanar acridine ring system render these PICs threading intercalators, directing the substituents into

134 formation and energy potentials derived from threading into a single score representing the relations

135 After threading into the SecYEG translocon, transmembrane segm

136 equest, fold recognition by prediction-based threading is available.

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

138 Threading is interrupted by pauses that are found to be

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

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

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

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

143 mologous template structures identified from threading, is described.

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

145 Whereas wrapping is less efficient than threading, it may have facilitated natural experimentati

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

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

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

149 Unlike FEN1, Dna2p shows evidence of a "threading-like" mechanism that does not support tracking

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

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

152 imers occurs in this fashion, indicates that threading may be an important phenomenon during protein

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

154 indings unravel the puzzling nature of how a threading mechanism can be used in the endoplasmic retic

155 h may have impeded heterodimer assembly by a threading mechanism, as observed when the hCG seatbelt w

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

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

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

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

160 de bond assignments and the fold recognition/threading method to search the Protein Data Bank found a

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

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

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

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

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

166 Threading methods extend coverage further into the twili

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

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

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

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

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

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

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

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

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

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

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

178 vement regarding structural details over the threading model.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

194 Threading of DNA through the central channel of a replic

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

196 The threading of monostoppered alkylbenzylammonium axles 7(+

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

226 erall C(2) symmetry, NMR analysis verified a threading polyintercalation mode of binding, with linker

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

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

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

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

231 n 365 cases, the templates identified by our threading program, PROSPECTOR_3, have a root-mean-square

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

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

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

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

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

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

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

239 The threading requirement prevents this active nuclease from

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

241 SP threading requires smaller forces when the SP is pulled

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

243 4 was synthesized in order to test this DNA-threading scenario.

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

245 only a predicted structure is available from threading servers.

246 The implemented multi-threading software FISH is freely available for academic

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

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

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

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

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

252 roadly applicable to many types of molecular threading systems.

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

254 an approach of homology-modeling and remote-threading techniques for the extramembranous domains usi

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

256 targets beyond the scope of current protein threading techniques.

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

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

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

260 through rearranging the rigid fragments from threading templates guided by a reduced Calpha and side-

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 study represents the first NMR analysis of a threading tetraintercalator and, as such, structurally c

267 tructural studies are reported for a modular threading tetraintercalator bound to DNA.

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

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

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

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

272 This explains why most hCG is assembled by threading the glycosylated end of alpha-subunit loop 2 b

273 re assembled in the endoplasmic reticulum by threading the glycosylated end of alpha-subunit loop two

274 s differs from hCG assembly, which occurs by threading the glycosylated end of loop alpha2 beneath th

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

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

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

278 Threading the NTD onto the AraC backbone revealed an alp

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

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

281 notube is dependent on the magnetic flux phi threading the tube.

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

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

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

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

286 SP threading through a nonallosteric ClpY nanopore involves

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

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

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

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

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

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

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

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

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

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

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

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

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