ライフサイエンスコーパス: homology model

1 ucture of a chimeric VLP and developed a VP1 homology model.

2 ith the proposed binding pose in a DAGLalpha homology model.

3 confirmed the binding modes predicted by the homology model.

4 ng a ligand-based focused library and a PLK4 homology model.

5 -GID and its analogs to an alpha4beta2 nAChR homology model.

6 hetic-binding cavity as observed in a TASK-3 homology model.

7 ue identity control helps to improve protein homology models.

8 forms of 6440 metabolites against these four homology models.

9 onal top-ranked cognate complexes when using homology models.

10 and-binding ectodomain to establish receptor homology models.

11 for each variant from crystal structures and homology models.

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 ity labeling, site directed mutagenesis, and homology modeling.

20 ical techniques, computational modeling, and homology modeling.

21 RY domains, which had been proposed based on homology modelling.

22 d structure or a close relative suitable for homology modelling.

23 The VP1 homology model allowed us predict the S domain (67-229)

24 Structural homology modeling allowed us to propose specific feature

25 tion of Kgp and RgpB, we derived a plausible homology model and mechanism of Kgp-regulating zymogenic

26 Docking studies with a NaV1.7 homology model and peptide NMR structure generated a mod

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

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

29 Homology modeling and biochemical analysis indicates tha

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

31 Homology modeling and computational docking studies indi

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

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

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

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

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

37 Homology modeling and in silico analysis of the GmSACPD-

38 Homology modeling and in silico mutagenesis suggests tha

39 Using homology modeling and ligand docking for binding pocket

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

41 Homology modeling and lipid-protein-overlay assays showe

42 Guided by homology modeling and molecular docking, we hypothesized

43 Homology modeling and molecular dynamics of the CslF6 pr

44 Homology modeling and molecular dynamics simulations sug

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

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

47 Using homology modeling and phylogenetic analyses, we present

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

49 Here we combine homology modeling and quantum chemical calculations with

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

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

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

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

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

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

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

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

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

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

60 r homologs related to oxidative stress by 3D-homology modelling and orthologous group comparisons.

61 Accurate SCR predictions can benefit homology modelling and sequence alignment.

62 Furthermore, using homology models and biochemical verifications, we show t

63 We used predictions from available homology models and crystal structures to modulate an ex

64 Finally, we present structural homology models and data from functional prediction soft

65 itionally difficult cases such as docking to homology models and ligand dependent domain rearrangemen

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

67 -randomly near the binding site of a GABAA-R homology model, and atomistic simulations were carried o

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

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

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

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

72 studies were done with sequence comparisons, homology modelling, and electrospray ionisation mass spe

73 sing a subset of analogues with DAT and SERT homology models, and functional data obtained with DAT (

74 atically generate antibody variable fragment homology models; annotate such models with estimated acc

75 ined either by experimental approaches or by homology modelling, are correlated with the size and sha

76 their structures, obtained via experiment or homology models, are provided.

77 docking large toxin peptides to ion channel homology models, as exemplified by the alpha-GID:alpha4b

78 using unbound, and 12% (2/17) when using the homology-modeled backbones to generate the complexes.

79 MD) simulations were performed using an A1AR homology model based on an agonist-bound A2AAR structure

80 molecular dynamics simulations on a hP2Y14R homology model based on P2Y12R structures.

81 porters, and computational docking in a BGT1 homology model based on the newly determined X-ray cryst

82 In particular, we construct homology models based on crystallographic structures of

83 ogs, we created in silico WT and AS PKCdelta homology models based on the crystal structure of PKCiot

84 high resolution structure of human P-gp, but homology models based on the crystal structures of bacte

85 ovide molecular insight, we constructed SERT homology models based on the Drosophila melanogaster dop

86 domain (TM) 10 and TM11/12 in NKCC1, testing homology models based on the structure of AdiC in the sa

87 Homology models based upon the high-resolution structure

88 The 5-HT3A receptor homology model, based on the partial structure of the ni

89 Homology models, based on the SAC1 structure from yeast,

90 We used a homology model-based approach to identify small-molecule

91 Homology model-based virtual screening, especially with

92 a(-) site, based upon the distance in GABAAR homology models between gamma2Ser-280 and beta3Met-227.

93 Homology modeling, bioinformatic analyses, and an assay

94 teins--including proteins for which reliable homology models can be generated--on the residue level h

95 A homology model capable of rationalizing these observatio

96 A novel homology model, comprehensive agonist and inhibitor titr

97 Homology modeling confirmed a critical role for the R213

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

99 Such homology modeling could prove useful in designing molecu

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

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

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

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

104 for binding of Rap1A and Rap1B, and present homology models examining the binding between Rap1A or R

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

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

107 Using homology modeling followed by docking, we identified key

108 We have generated a homology model for GLUT4 that we utilized to screen for

109 The structures were also used to generate a homology model for the human homolog hASNase1 and to hel

110 Fitting of this SCP model and a homology model for the MCP upper domain into the cryoEM

111 Homology models for hBI-1 provide insights into TMBIM-me

112 , using cell-based assays, and compared with homology models for these hGLUT members.

113 Using a homology model, four residues (N251, A263, I299, and F38

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

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

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

117 Several CFTR homology models have been developed using bacterial ABC

118 0 conformationally distinct ROMK comparative homology models identified two putative binding sites in

119 Computer docking into a ScPma1p homology model identifies a binding mode that supports g

120 Homology modeling illustrates modes of resistance result

121 on chemokine receptor crystal structures and homology models illustrates the possibilities and challe

122 ormation, we constructed a three-dimensional homology model in which the alpha565 trimer shows a good

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

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

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

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

127 Homology modeling is a powerful tool for predicting a pr

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

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

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

131 Using in silico homology modelling, molecular docking and mutagenesis st

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

133 The homology model of a putative pentalenene synthase (Unipr

134 To rationalize these results, a homology model of a receptor-ligand complex was built us

135 d substrate specificity, we also generated a homology model of a related ortho-hydroxylase (C2'H) fro

136 Molecular modeling studies using a homology model of a single rat TRPM8 subunit identified

137 Here we present a homology model of BbMAT that has the standard major faci

138 that validate the newly developed structural homology model of CNT membrane architecture for human CN

139 When mapped onto a homology model of DBLbeta3_D4, these cluster to a define

140 The 3D homology model of each PLA2 displays a binding pocket th

141 arisons of X-ray crystal structures with the homology model of GAS; a triad [Thr 401-Gly 402-Gly 403]

142 the GAT1 inhibitor tiagabine into a protein homology model of GAT1 allowed derivation of a common bi

143 binding and the amino terminal domains in a homology model of GluN1/GluN2C built from crystallograph

144 we identified small molecule ligands using a homology model of GPR171 to virtually screen a library o

145 A homology model of hBest1 shows the locations of disease-

146 ransporter VcINDY, from which we generated a homology model of human NaPi-IIa.

147 molecules were docked into a newly developed homology model of human NPP1.

148 Employing a homology model of KCa3.1, we first determine conduction

149 eting, especially because design relied on a homology model of M3P6.

150 D382V and place nine affected residues on a homology model of PAT-4.

151 t the glycerol 3-phosphate transporter-based homology model of PCFT and the presence of an extracellu

152 A homology model of PCFT, based upon theEscherichia coligl

153 tion attenuates PKG activity, we developed a homology model of PKG-1alpha.

154 A structure-guided design approach using a homology model of Plasmodium falciparum calcium-dependen

155 nt with the SAR data was proposed based on a homology model of SIRT2.

156 equence structure guided approach based on a homology model of Smlt1473 to identify nine putative sub

157 The homology model of sstr2 was built and was used to aid th

158 o acid transporter of the APC superfamily, a homology model of STM2200 was created.

159 in the vicinity of the TARGSQQY peptide in a homology model of TBB3 predicted a binding pose and conf

160 On the basis of a homology model of the 35-amino acid NTR of MYO1C(35) (NT

161 spBHI recognition preference, we generated a homology model of the AspBHI-DNA complex, and probed the

162 cture of the T4CP holocomplex by combining a homology model of the ATPase domain of DotL.

163 Based on this information, a homology model of the B. subtilis tau3-delta-delta' comp

164 LV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD).

165 Docking of commercial libraries into a homology model of the enzyme has led to the discovery of

166 panning and cytoplasmic domains, serves as a homology model of the extracellular domain of the nAChRs

167 ocations of the mutations were mapped onto a homology model of the flounder protein.

168 al domain from Chaetomium thermophilum and a homology model of the human tuberin N terminus are prese

169 b1) and used these coordinates to generate a homology model of the intramolecular interaction that in

170 A homology model of the MERS-CoV PLpro structure was gener

171 A homology model of the nucleotide-activated P2Y2R was cre

172 A homology model of the PilQ protein was fitted into the c

173 rse set of BAM2 orthologs were mapped onto a homology model of the protein, revealing a large, conser

174 making it difficult to generate an accurate homology model of the protein.

175 receptor was analyzed in detail using the 3D homology model of the sigma1 receptor.

176 molecular dynamics simulations based on a 3D homology model of the sigma1 receptor.

177 A homology model of the VP1 indicated for the first time t

178 According to a homology model of the yeast hexose transporter Gal2 dedu

179 lastin binding site of human EBP, we built a homology model of this protein and docked VGVAPG on its

180 c resonance structure of [C117S]YmoB and the homology model of TomB show that the two proteins form a

181 terpreted consistently in the context of the homology model of TRPV4 molecule we have developed and r

182 m tarantula myosin to build a single-species homology model of two heavy meromyosin interacting-heads

183 Here we present a homology model of VMAT2, which has the standard MFS fold

184 for the localization defect, we developed a homology model of zebrafish Abcc4.

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

186 Homology modeling of Aspergillus fumigatus DHODH has ide

187 Homology modeling of BjNRAMP4.1 suggested that it could

188 Homology modeling of its major structural subunit, CotA,

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

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

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

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

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

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

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

196 Homology modeling of the protein F tertiary structure re

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

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

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

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

201 ious CaCC structural analyses have relied on homology modelling of a homologue (nhTMEM16) from the fu

202 ons, we have now developed a pipeline for 3D homology modelling of domains in Gene3D.

203 Homology modelling of the OSM-9 pore suggests that Y(604

204 We construct homology models of a human GABAAR based on the structure

205 plar antagonists from two chemical series to homology models of both human and mouse Free Fatty Acid

206 e crystal structures of ABC transporters and homology models of CFTR.

207 al homolog in various conformations, derived homology models of eukaryotic neurotransmitter transport

208 If virtual screening against homology models of GPCRs could be used to identify fragm

209 Homology models of hNTPDase1 and -2 were constructed.

210 uum membrane-bending analysis carried out on homology models of mammalian homologs shows that these f

211 r structures as a guide, we have constructed homology models of several of these "X-succinate synthas

212 The method constructs homology models of TFs bound to DNA and assesses the rel

213 docking to screen >500000 fragments against homology models of the A3 and A1 adenosine receptors (AR

214 ant set of antibody-antigen complexes and on homology models of the antibodies and/or the unbound ant

215 The CFTR structure is unsolved but homology models of the CFTR closed and open states have

216 On the basis of the new findings and homology models of the closed and open conformations of

217 Finally, homology models of the cytochrome b protein revealed a s

218 6 (TMD) was subsequently utilized in docking homology models of the ECD and the TMD to create a full-

219 intermolecular contacts, allowing us to fit homology models of the individual domains into the SAXS-

220 Homology models of the larval An. gambiae ACE proteins (

221 Here we present homology models of the murine AhR:ARNT PAS domain dimer

222 these observations, we generated structural homology models of the N-linked glycoproteome of C. jeju

223 Homology models of the open and closed states of P2X2 in

224 Specifically, we built homology models of the three antibody-gp120 complexes, e

225 Rigid body fitting of homology models of these SMP domains in the density maps

226 Based on docking of polyols to homology models of transporters, we propose the architec

227 inding cysteine-rich domain of Fn14, several homology models of TWEAK were built to investigate plaus

228 Wnt-Frizzled CRD interactions, we generated homology models of Wnt-Frizzled CRD interactions and dev

229 PNPase-RNase Y interaction were guided by a homology model ofB. subtilisPNPase based on the known st

230 ered molecular dynamics (SMD) simulations on homology models offered insight into the process of cohe

231 improved the quality and coverage of our 3D homology modelling pipeline of predicted CATH domains.

232 PfCPSF3 homology models placed these mutations in the active sit

233 Potassium channel-based homology models predict amino acid Ile-1575 in domain IV

234 Homology models predict that the ligand-binding pockets

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

236 L1 crystallographic homology models predicted a degree of structural diversi

237 Homology modeling predicts protein structures using know

238 Homology modeling predicts that position 596 directs pro

239 Structural homology modeling predicts that this protease adopts a f

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

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

242 s in a Mycobacterium tuberculosis (Mtb) GyrB homology model prompted exploration of the side chains a

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

244 important subject with clear applications in homology modelling, protein structure prediction, protei

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

246 odel used to infer the rates, the ability to homology-model query proteins, prediction of the seconda

247 Homology modeling revealed glutamyl and aspartyl residue

248 Site-directed mutagenesis and homology models show the importance of a halogen bond in

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

250 A predicted three-dimensional homology model shows that all the TMSs, apart from TMS4

251 Homology modeling shows that the scramblase domain forms

252 Current homology modelling software is optimized for globular pr

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

254 Protein homology modeling studies showed significant structural

255 Homology modelling, substrate docking, molecular dynamic

256 The homology model suggested that the bulky methionine subst

257 Homology modeling suggested alterations in the class I a

258 Homology modeling suggested that the Glu-221 side chain

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

260 Homology modeling suggested that the structure of region

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

262 These data, in addition to a new homology model, suggested that a conformational change i

263 n silico docking using a GLIC closed channel homology model suggests propofol binds to intersubunit s

264 Protein homology modelling suggests that four amino acid substit

265 Molecular docking to nAChR subtype homology models suggests agonist specific interactions t

266 Here, homology modeling supported the alternating access trans

267 re of full-length PAH supersedes a composite homology model that had been used extensively to rationa

268 ent with in silico docking calculations in a homology model that orient the long axis of etomidate ap

269 g was supported by three-dimensional protein homology models that predict a plausible recognition sit

270 In this study, we use an EAAT3 homology model to calculate the pKa of several titratabl

271 Selected analogues were docked to an A3AR homology model to explore the environment of receptor-bo

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

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

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

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

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

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

278 king, surface accessibility measurements and homology modelling to define subunit stoichiometry and i

279 r dynamics simulations of adult versus fetal homology models to identify complementary-subunit residu

280 ap still primarily rely on fitting atomic or homology models to the density map.

281 Molecular modeling studies on a PDGF-Rbeta homology model using prediction of water thermodynamics

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

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

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

285 A receptor homology model was built and docking studies were perfor

286 Via homology modelling we predicted and confirmed an integra

287 Using homology models we derived, high-throughput virtual scre

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

289 By homology modeling, we identified the corresponding L596-

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

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

292 aid of previously determined structures and homology modelling, we derive a pseudo-atomic structure

293 InterPro sequence signatures and homology modelling were then used to assess our sample o

294 Moreover, homology models were generated for the catalytic domains

295 More than 3,000 GPR68 homology models were refined to recognize lorazepam in a

296 The updated homology models will be useful for virtual screening and

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

298 In homology modeling with other calpains, this R243L CAPN5

299 full-length LRRK2 by combining domain-based homology models with multiple experimental constraints p

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