ライフサイエンスコーパス: homology modeling

1 ity labeling, site directed mutagenesis, and homology modeling.

2 ical techniques, computational modeling, and homology modeling.

3 problem of accurate loop refinement for GPCR homology modeling.

4 abling prediction of the VZV gH structure by homology modeling.

5 ignments of multiple template structures and homology modeling.

6 ructure-based PPI predictions that go beyond homology modeling.

7 in this case by electron cryomicroscopy and homology modeling.

8 renergic receptor was used as a template for homology modeling.

9 models of mid-range quality based on remote homology modeling.

10 d T. thermophilus Ndx1, were generated using homology modeling.

11 by using site-directed mutagenesis and CCR5 homology modeling.

12 otein was available, a 3D model was built by homology modeling.

13 p analogues using fluorescence titration and homology modeling.

14 structure determination and inaccessible to homology modeling.

15 into these kinetic differences acquired via homology modeling.

16 states of the CFTR gating cycle by means of homology modeling.

17 combination of cryo-electron microscopy and homology modeling.

18 ural models for the RbTI were predicted with homology modeling.

19 heir function(s), despite their discovery by homology modeling a decade ago.

20 Using homology modeling, a VCOP mutant with two substitutions

21 mined crystallographically were predicted by homology modeling according to the amino acid sequence.

22 Structural homology modeling allowed us to propose specific feature

23 o a degree that was not possible with static homology modeling alone and provided a deeper rationaliz

24 Homology modeling analysis suggests that the inhibitory

25 tudy demonstrates that the integrated use of homology modeling and a multiscale refinement protocol t

26 Here, homology modeling and a new simulation method developed

27 tructural-functional classification based on homology modeling and a search for diagnostic catalytic

28 is essential for a variety of tasks such as homology modeling and active site prediction.

29 We used homology modeling and analyses of the solution and membr

30 processes has been studied effectively using homology modeling and applied to ligand design.

31 Homology modeling and biochemical analysis indicates tha

32 Homology modeling and comparative analysis of NepR, PhyR

33 Homology modeling and comparative structural analyses of

34 thod to predict these interactions, based on homology modeling and computational docking of the virus

35 Homology modeling and computational docking studies indi

36 and the TK2 clade of vertebrates followed by homology modeling and discrete molecular dynamics calcul

37 hich can account for uncertainty inherent in homology modeling and docking by producing statistical d

38 Results obtained from homology modeling and docking explain the observed selec

39 leverages available structural data through homology modeling and docking of possible products into

40 finity and efficacy could be rationalized by homology modeling and docking of these hypermodified nuc

41 s of deduced amino acid sequence, phylogeny, homology modeling and docking simulation.

42 We used homology modeling and docking studies to guide fragment

43 six mutant receptors in vitro and then used homology modeling and dynamic simulation to predict drug

44 Homology modeling and in silico analysis of the GmSACPD-

45 igand-receptor binding mode prediction using homology modeling and in silico docking approaches.

46 Homology modeling and in silico mutagenesis suggests tha

47 ane-binding proteins through high throughput homology modeling and in-depth calculation of biophysica

48 Using homology modeling and ligand docking for binding pocket

49 By using in silico homology modeling and ligand docking, we provide insight

50 Homology modeling and lipid-protein-overlay assays showe

51 enzymes by computational methods, including homology modeling and metabolite docking, which suggeste

52 Guided by homology modeling and molecular docking, we hypothesized

53 Homology modeling and molecular dynamics of the CslF6 pr

54 Homology modeling and molecular dynamics simulation stud

55 Homology modeling and molecular dynamics simulations sug

56 nctional studies are supported by structural homology modeling and molecular dynamics simulations, su

57 Here, by integrating homology modeling and molecular dynamics, we generated a

58 Homology modeling and molecular mechanics were used to b

59 properties of green proteorhodopsin by using homology modeling and molecular orbital theory.

60 Homology modeling and mutagenesis experiments suggest th

61 Homology modeling and mutagenesis identified a cluster o

62 Homology modeling and mutagenesis study showed that the

63 Homology modeling and mutational analysis demonstrated a

64 netic studies in combination with structural homology modeling and NMR spectroscopic analyses to iden

65 Using homology modeling and phylogenetic analyses, we present

66 hepatitis E virus capsid model, we performed homology modeling and produced a complete, T = 3 astrovi

67 d be a significant advance for the fields of homology modeling and protein design.

68 studies demonstrate the potential utility of homology modeling and protein structure analysis for eng

69 Template-based modeling, including homology modeling and protein threading, is the most rel

70 Here we combine homology modeling and quantum chemical calculations with

71 Homology modeling and rat PK/PD studies on benchmark com

72 iamine pyrophosphate and Mg(2+) was built by homology modeling and refined by molecular dynamics simu

73 -electron microscopy density-map-constrained homology modeling and refinement.

74 rmance of the constrained de novo method for homology modeling and rigid-body docking and present the

75 Furthermore, homology modeling and SAXS allowed the construction of a

76 Homology modeling and scanning cysteine mutagenesis stud

77 Using homology modeling and site-directed mutagenesis, hNK(1)-

78 To investigate this further, we used homology modeling and structural comparison to identify

79 gions of experimental structures, useful for homology modeling and structure prediction of receptors.

80 Through the use of homology modeling and structure threading, NDR1 was pred

81 Using homology modeling and structure-based design, specific s

82 ndem Winged-Helix domains [6], and, by using homology modeling and structure-function analysis, we id

83 The predicted three-dimensional homology modeling and substrate docking suggested the pr

84 structure of the pro-domain was obtained by homology modeling and suggested that a pro-peptide Lys r

85 of the RyR1 pore-forming region, obtained by homology modeling and supported by mutational scans, ele

86 improved interface alignments should enhance homology modeling and threading methods for predicting P

87 ized into template-based modeling (including homology modeling and threading) and free modeling.

88 of ECE2 that we had identified previously by homology modeling and virtual screening of a library of

89 nnel crystal structures (templates for KCNQ1 homology-modeling) and KCNE1 NMR structures.

90 de transport with site-directed mutagenesis, homology modeling, and [(3)H]adenosine flux measurements

91 tudy, we utilized site-directed mutagenesis, homology modeling, and assays with a peptide library to

92 with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an in

93 a combination of site-directed mutagenesis, homology modeling, and ligand-docking simulations to ana

94 aled by mass spectrometry of dimer subunits, homology modeling, and molecular dynamics simulation.

95 g mutagenesis of AuIB and alpha3beta4 nAChR, homology modeling, and molecular dynamics simulations to

96 chain repacking, including x-ray refinement, homology modeling, and protein design, the accuracy limi

97 n protein-protein interaction trap strategy, homology modeling, and site-directed mutagenesis, we ide

98 plications for protein structure refinement, homology modeling, and structure prediction.

99 A ligand-steered homology modeling approach has been developed (where inf

100 provides an improvement over single-template homology modeling, as evaluated by the accuracy of rigid

101 Functional data and homology modeling assisted identification of critical am

102 ty of receptor-bound C2 groups was probed by homology modeling based on recent X-ray structure of an

103 Three-dimensional homology modeling based on the crystal structure of YiiP

104 Homology modeling based on the ING4 structure suggests t

105 Homology modeling, bioinformatic analyses, and an assay

106 Homology modeling combined with in silico docking of lys

107 tive approach of multi-resolution filtering, homology modeling, computational simulation of mismatche

108 Homology modeling confirmed a critical role for the R213

109 We sought to determine whether homology modeling could identify putative determinants o

110 Such homology modeling could prove useful in designing molecu

111 -repeat bivalent tetramer was produced using homology modeling coupled with chemical cross-linking.

112 ure of the heterodimer initiation site using homology modeling coupled with structural refinement bas

113 veloped a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrome

114 Activity profiling, complex isolation, and homology modeling data revealed unique interactions of R

115 e-directed mutagenesis of GPR81 coupled with homology modeling demonstrates that classically conserve

116 electrophysiological analysis, together with homology modeling, demonstrates that W583 is part of the

117 etta also has methods for molecular docking, homology modeling, determining protein structures from s

118 g of BSS, a computational approach involving homology modeling, docking studies, and molecular dynami

119 TM) methods, including protein threading and homology modeling, especially when the sequence identity

120 lin and the other ovodefensins calculated by homology modeling exhibit atypical hydrophobic surface p

121 Many applications, such as protein design, homology modeling, flexible docking, etc. require the pr

122 Using homology modeling followed by docking, we identified key

123 Using molecular homology modeling for Tob55 and cryoelectron microscopy

124 COG2252 genes of Escherichia coli K-12 with homology modeling, functional overexpression, and mutage

125 advances in the structural biology of GPCRs, homology modeling has been carried out to rationalize bi

126 the 398 membrane proteins, while those from homology modeling have TMscore>0.5 for only 10 of them.

127 Homology modeling identifies striking similarities betwe

128 Homology modeling illustrates modes of resistance result

129 e recognition of FasL using a combination of homology modeling, immunoprecipitation, hydrogen-deuteri

130 Here, using homology modeling in combination with mutagenesis and el

131 g evolutionary trace analysis and structural homology modeling in conjunction with site-directed muta

132 Using homology modeling in conjunction with site-directed muta

133 ard such distortions, as observed for remote homology modeling in the latest CASP8 (Comparative Asses

134 the purified recombinant protein, molecular homology modeling, in vivo stable isotope labeling, and

135 nctional studies, extensive mutagenesis, and homology modeling indicate the following mechanism.

136 cation in melanoma-associated antibodies and homology modeling indicated differential potential antig

137 Mechanistically, homology modeling indicated that the beta3-alpha3 loop d

138 Bioinformatics and homology modeling indicated that the MotB proteins of T.

139 Homology modeling indicated that the mutation altered sa

140 Homology modeling indicated the presence of the conserve

141 Homology modeling indicates that As(III) binding sites i

142 Homology modeling indicates that Asn-32 and Asn-104 are

143 Homology modeling indicates that Pro(392) may play an im

144 Homology modeling indicates that the HARP domain is simi

145 Three-dimensional homology modeling indicates that the side chains of Gln-

146 Homology modeling is a powerful tool for predicting a pr

147 erived structure-activity relationships with homology modeling leads to new detailed insights in the

148 Using homology modeling, ligand docking, and molecular dynamic

149 based virtual screening strategy, comprising homology modeling, ligand-support binding site optimizat

150 Homology modeling localized His247 to the large loop sep

151 an interdisciplinary approach that included homology modeling, MD simulations, and biophysical and b

152 Clearly, the ligand-steered homology modeling method reduces the uncertainty of stru

153 Current homology modeling methods for predicting protein-protein

154 ngineering of new alpha4beta2-nAChR ligands, homology modeling methods, combined with in silico ADME

155 By performing homology modeling, molecular docking, and molecular dyna

156 Using structure-activity, homology modeling, molecular docking, and mutagenesis st

157 gated via cryogenic electronic spectroscopy, homology modeling, molecular dynamics, and molecular orb

158 By combining homology modeling, molecular dynamics, cysteine cross-li

159 As was expected from homology modeling, mutation of three TM5 serine residues

160 Together with homology modeling, mutational data, quantum mechanical c

161 sigma values by performing the single-domain homology modeling of 22 CASP9 targets and 24 CASP10 targ

162 Homology modeling of ABCG2 places the TXXXGXXXG motif at

163 Homology modeling of Aspergillus fumigatus DHODH has ide

164 Homology modeling of BjNRAMP4.1 suggested that it could

165 Protein homology modeling of both the AGPATs with glycerol-3-pho

166 Thus, homology modeling of GPCRs remains a useful technique in

167 Homology modeling of human SERT (hSERT), based on high r

168 Homology modeling of its major structural subunit, CotA,

169 Homology modeling of m-tomosyn-1 based on the known stru

170 he highest impact as potential templates for homology modeling of other GPCRs, if their structures we

171 In this work, we used homology modeling of OX receptors to direct further SDM

172 sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, ou

173 data can be used as a powerful constraint in homology modeling of protein structures.

174 Homology modeling of SIRPalpha.D1 revealed topological r

175 P variants to peptide selection, we combined homology modeling of TAP with experimental measurements

176 These findings were combined with homology modeling of the A1 receptor and in silico scree

177 Homology modeling of the beta(2) subunit using the cryst

178 NMR binding studies in combination with homology modeling of the bound beta-mannan antigen sugge

179 Interestingly, our biochemical data and homology modeling of the CAT domain suggest that Arg-285

180 Protein homology modeling of the deduced novel mutations (P35 de

181 of the mutations were rationalized based on homology modeling of the Dmp53 DNA-binding domain, sugge

182 l fold of the domains and were used to guide homology modeling of the ECD.

183 Homology modeling of the full-length Limenitis arthemis

184 of evolutionary and biochemical analyses and homology modeling of the Galpha and RGS proteins to addr

185 Homology modeling of the human A(2A) adenosine receptor

186 Homology modeling of the KCNQ1 channel based on the Kv1.

187 Homology modeling of the mispair-binding domain (MBD) of

188 Finally, we performed homology modeling of the pore region of wild-type and mu

189 the effects of these mutations, we performed homology modeling of the pore region of wild-type and mu

190 Homology modeling of the protein and its oligosaccharide

191 Homology modeling of the protein F tertiary structure re

192 In this study, we used homology modeling of the rat P2X2 receptor with the zebr

193 Homology modeling of the RbgA switch I region using the

194 In addition, homology modeling of the receptor and docking studies fo

195 Homology modeling of the RSK2 NH(2)-terminal domain and

196 Homology modeling of the sensing domain of the B. subtil

197 alytic residues were shown to be proximal by homology modeling of the SHFV nsp1s on porcine respirato

198 Sequence comparisons and homology modeling of the structures identify a few key a

199 the former prototypic rhodopsin template for homology modeling of the transmembrane (TM) region of hu

200 Homology modeling of UGT2B7 with related plant flavonoid

201 Homology modeling of UNC-89's SH3 suggests structural fe

202 Homology modeling of YdgR, Cam docking, and mutational s

203 corroborated by the conservation pattern and homology modeling on the recently described x-ray struct

204 alysis of the cognate gp120 sequence through homology modeling places this potential epitope near the

205 ates with a specificity similar to APTs, and homology modeling points toward an APT-like enzyme.

206 49)]) is similar in sequence to the Sir1OIR; homology modeling predicted a structure for Sir1(27-149)

207 residue for Rab-GAP function, and in silico homology modeling predicted impaired GAP function in the

208 Homology modeling predicted Nan KLF1 binds CACCC element

209 Homology modeling predicted the binding conformation of

210 Homology modeling predicts protein structures using know

211 Homology modeling predicts that phosphorylation at T131

212 Homology modeling predicts that position 596 directs pro

213 Structural homology modeling predicts that this protease adopts a f

214 Homology modeling predicts that WDR-23 folds into a beta

215 o X. laevis AHRs (A364, A380, and N335), and homology modeling predicts they protrude into the bindin

216 is important for many applications including homology modeling, protein docking, and for placing smal

217 Using a combination of homology modeling, protein-protein interaction, and kina

218 data combined with biophysical analyses and homology modeling provide a molecular understanding of t

219 ifugation, small-angle x-ray scattering, and homology modeling provide insight into TNPO3 architectur

220 Homology modeling revealed conserved three-dimensional s

221 Homology modeling revealed glutamyl and aspartyl residue

222 Structural homology modeling revealed that several of the BCL11B mu

223 NMR structural determinations, combined with homology modeling, revealed that SkIgC4 and SkIgC5 both

224 Homology modeling reveals that the beta4-beta5 linker ph

225 Furthermore, our homology modeling reveals that the Vif Cullin box and zi

226 icella-zoster virus (VZV) gB is limited, but homology modeling showed that the structure of VZV gB wa

227 Sequence alignment and homology modeling showed that the subtype-specific effec

228 Homology modeling shows that the scramblase domain forms

229 vity relationship, pharmacological analysis, homology modeling, species ortholog comparisons, and mut

230 Protein homology modeling studies showed significant structural

231 Experimental data and homology modeling suggest a structure for the exofacial

232 X-ray diffraction studies and homology modeling suggest that their N-terminal regions

233 Homology modeling suggested alterations in the class I a

234 of ORF16 eliminated pigment production, and homology modeling suggested that ORF16 shares a structur

235 Homology modeling suggested that the Glu-221 side chain

236 Sequence conservation and homology modeling suggested that the insertion in the gu

237 Homology modeling suggested that the structure of region

238 sed on MHC-II eluted peptides and structural homology modeling suggested that variants in the RT1-B P

239 Comparative homology modeling suggested the active site residues Asp

240 Structure homology modeling suggested the involvement of several a

241 Homology modeling suggests that gamma(2)Arg43, gamma(2)G

242 Homology modeling suggests that most architectural nucle

243 utations are within a conserved BACK domain; homology modeling suggests that mutant amino acid side c

244 Homology modeling suggests that the effects of the F344

245 In agreement with our findings, homology modeling suggests that the very C-terminal resi

246 Structural homology modeling suggests this Nab3 'tail' forms an alp

247 Here, homology modeling supported the alternating access trans

248 Homology modeling supports the concept that the ADPH C t

249 Structure-based drug design combined with homology modeling techniques were used to develop potent

250 alytic (CAT) domain or residues predicted by homology modeling to be close to DNA in the core-binding

251 of Cys124 and Cys152, residues indicated by homology modeling to be in close proximity and in the pr

252 ining an alpha4(D204C) mutation predicted by homology modeling to be within reach of the reactive pro

253 The distal end of the chain was predicted by homology modeling to bind at the A(3)AR extracellular re

254 We have used homology modeling to construct a model of the N-terminal

255 We use parallel homology modeling to expand the current PTP structure sp

256 This experimental data set was used in homology modeling to guide the positioning of the angiot

257 Here, we used homology modeling to identify a conserved STIM1(448-530)

258 urrent study, we used sequence alignment and homology modeling to identify features common to nonturr

259 otein Data Bank code 3F7T) as a template for homology modeling to identify key amino acids of Arabido

260 Here we use molecular biology and homology modeling to identify residues that line a candi

261 Tyr-418, two residues that are predicted by homology modeling to lie within 2.8 A of each other at t

262 A site-directed mutagenesis study, guided by homology modeling to LuxR and TraR, has revealed three c

263 Here, we use calculations of pK(A)s and homology modeling to predict the location of a functiona

264 In addition, we used homology modeling to predict the S1, S2, and S4 subsite

265 inding, voltage clamp electrophysiology, and homology modeling to probe the role of two residues in l

266 of the PG9 light chain at 3.0 A facilitated homology modeling to support the presence of these unusu

267 Based on three-dimensional homology modeling to the Meiothermus ruber subunit I, we

268 nal model of cohesin has been constructed by homology modeling using both crystallographic and electr

269 nsional model of the structure of cpSRP54 by homology modeling using cytosolic homologs.

270 structural models of human MFSD2A derived by homology modeling using MelB- and LacY-based crystal str

271 ecular models of the CFTR pore: one based on homology modeling using Sav1866 as the template and a se

272 ilicum gamma-cadinene synthase were built by homology modeling using the template structure of Gossyp

273 a graphical interface for basic comparative (homology) modeling using SCWRL and other programs.

274 nd (2) the extent to which multiple-template homology modeling (using all currently available GPCR cr

275 Ligand-guided homology modeling was applied to wild type receptors and

276 Homology modeling was first used to generate a starting

277 crystal structures of component proteins and homology modeling, we constructed a nearly complete, pse

278 servations, multiple sequence alignment, and homology modeling, we constructed structural models for

279 By homology modeling, we demonstrated that the loss-of-func

280 Using sequence alignments and homology modeling, we designed a DDR2 construct appropri

281 Through homology modeling, we found that MET and GCE possess a C

282 By dynamic homology modeling, we further hypothesized that the cond

283 Furthermore, through molecular homology modeling, we have proposed a mechanism for the

284 Based on homology modeling, we hypothesized that the proximal reg

285 Based on our crystal structures and homology modeling, we identified five amino acids surrou

286 By homology modeling, we identified the corresponding L596-

287 By homology modeling, we identified two Glu residues (Glu-1

288 Using template-based structural homology modeling, we now show that the ectodomain of HA

289 Using MD simulations based on homology modeling, we observe that the carbonyl of the f

290 Using structural homology modeling, we propose that phosphorylation on Ty

291 cted mutagenesis complemented with in silico homology modeling, we report the binding modes of two hi

292 Using homology modeling, we show that these amino acids are po

293 This preference was confirmed by homology modeling, which revealed a shallow, hydrophobic

294 large improvement room for multiple template homology modeling while several other MSA tools fail to

295 In this paper, we combine homology modeling with coarse-grained (CG) and all-atom

296 eveloped a novel, hybrid approach, combining homology modeling with evolutionary coupling constraints

297 Homology modeling with molecular mechanics and molecular

298 In homology modeling with other calpains, this R243L CAPN5

299 for protein sequence-structure analysis and homology modeling within the interactive visualization c

300 rthemore, ab initio shape reconstruction and homology modeling would suggest that-in the deletion mut