ライフサイエンスコーパス: homology model

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

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

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

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

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

6 and-binding ectodomain to establish receptor homology models.

7 for each variant from crystal structures and homology models.

8 ue identity control helps to improve protein homology models.

9 n with newly constructed mA(3)AR and hA(3)AR homology models.

10 sense variants can be effectively applied to homology models.

11 e shifts for the RRM2,3 isolated domains and homology modeling.

12 into these kinetic differences acquired via homology modeling.

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

14 yo-EM), cross-linking mass spectrometry, and homology modeling.

15 p analogues using fluorescence titration and homology modeling.

16 structure determination and inaccessible to homology modeling.

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

18 combination of cryo-electron microscopy and homology modeling.

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

20 eriments, mutagenesis, ELISA, and structural 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 Homology modeling also showed that among some, but not a

26 Results from homology modeling analyses suggest that the unusual stru

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

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

29 A combined in silico hA(3)AR-homology model and site-directed mutagenesis study was p

30 ulations with an alpha7 extracellular domain homology model and two acetylcholine-binding protein hom

31 the Lys-5 target site), we generated an EftM homology model and used it in protein/protein docking st

32 Our study used homology modeling and a coarse-grained model to generate

33 its entries, making it a useful resource for homology modeling and active site identification studies

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

35 Using homology modeling and binding and contractility assays w

36 Homology modeling and biochemical analysis indicates tha

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

38 Homology modeling and computational docking studies indi

39 dies, and these studies are supported by MCT homology modeling and computational inhibitor-docking st

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 Homology modeling and in silico analysis of the GmSACPD-

43 Homology modeling and in silico mutagenesis suggests tha

44 Using homology modeling and ligand docking for binding pocket

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

46 Homology modeling and lipid-protein-overlay assays showe

47 Guided by homology modeling and molecular docking, we hypothesized

48 Homology modeling and molecular dynamics of the CslF6 pr

49 s, we developed a new approach that combined homology modeling and molecular dynamics simulations to

50 -carbonic and gamma-carbonic anhydrases, and homology modeling and molecular dynamics simulations wer

51 ture was solved using a novel combination of homology modeling and molecular replacement.

52 Homology modeling and normal mode analysis demonstrated

53 Using homology modeling and phylogenetic analyses, we present

54 Here we combine homology modeling and quantum chemical calculations with

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

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

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

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

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

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

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

62 pseudogenes linked to HPs, homology modelling and non-coding RNAs associated to HPs

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

64 s is one of the first examples of the use of homology modelling and protein docking for affinity matu

65 Homology modelling and sequence alignment analysis furth

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

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

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

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

70 e allosteric modulator (NAM) by mutagenesis, homology modeling, and competition studies with positive

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

72 vious structural data of individual domains, homology modeling, and flexible fitting to SAXS data usi

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

74 his result, together with sequence analysis, homology modeling, and SAR, allows us to propose CPD4 as

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

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

77 s for the differences based on a full-length homology modeling approach.

78 orresponding P2Y(14)R region is predicted by homology modeling as a deep, sterically limited hydropho

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

80 with the receptor based on a conformational homology modeling associated with docking simulations.

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

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

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

84 A homology model based on the Bombyx mori EH crystal struc

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

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

87 es can be broken by mutations designed using homology models based on Dpr and DIP structures.

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

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

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

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

92 tures and slightly fewer of those mapping to homology models being within 30 angstrom.

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

94 Homology modeling, bioinformatic analyses, and an assay

95 ular dynamics (MD) simulations with a UGT2B7 homology model can be used to identify critical binding

96 A homology model capable of rationalizing these observatio

97 isms underlying nAChR lipid sensing, we used homology modeling, coevolutionary analyses, site-directe

98 Homology modeling, combined with a recently reported cry

99 n its nucleotide-free state and a derivative homology model containing 61 amino acid substitutions un

100 class for pharmaceutical therapies in which homology modeling could fill the knowledge gap for struc

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

102 Such homology modeling could prove useful in designing molecu

103 also showed the mutant structures created by homology modeling could reproduce the difference of dyna

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

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

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

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

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

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

110 Using homology modeling followed by docking, we identified key

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

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

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

114 of LBDs from nonplant species and generated homology models for other GLR isoforms.

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

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

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

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

119 Several CFTR homology models have been developed using bacterial ABC

120 0 conformationally distinct ROMK comparative homology models identified two putative binding sites in

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

122 Homology modeling illustrates modes of resistance result

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

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

125 y using nondenaturing MS, cross-linking, and homology modeling in which EtfA, -B, and -C each contain

126 Sequence analysis and homology modelling indicate that Rv2509 belongs to the s

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

128 rRpm1 induces phosphorylation of AtRIN4, but homology modeling indicated that AvrRpm1 may be an ADP-r

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

130 Furthermore, docking into human HDAC10 homology models indicated that a hydrogen bond between a

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

132 which a near-atomic-resolution structure or homology model is available.

133 of improved threading algorithms for remote homology modeling is a critical step forward in template

134 Homology modeling is a powerful tool for predicting a pr

135 Homology modeling is used to bridge this gap but relies

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

137 onclude by pointing out that a single static homology model may not be adequate for predicting hydrop

138 Receptor usage information and homology models may be useful for predicting V3 loop bnA

139 Knowledge of receptor usage and homology models may be useful in developing future algor

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

141 Homology modeling, molecular dynamics simulations, and l

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

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

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

145 bcellular localizations, haplotypes, protein homology modeling, mutational, and expression analyses.

146 erent and complementary techniques including homology modeling, network theory, and machine learning.

147 The homology model of a putative pentalenene synthase (Unipr

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

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

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

151 We performed ligand docking studies to a homology model of AtABCC2 and probed the putative bindin

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

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

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

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

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

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

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

159 A homology model of GPR84 was generated to perform docking

160 Utilizing a homology model of human EAAT2, we identified a binding p

161 Computational docking to a homology model of human P2X4, based on the open state of

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

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

164 A homology model of PCFT, based upon theEscherichia coligl

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

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

167 Using a homology model of ScBOR1p, we identified a possible lipi

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

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

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

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

172 tional approach for molecular docking to the homology model of the AhR LBD that includes the receptor

173 work, we docked members of this family to a homology model of the alpha7 receptor extracellular doma

174 ybridoma derived antibody, AB1, using just a homology model of the antibody fragment variable region

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

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

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

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

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

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

181 In this study, a three-dimensional homology model of the M013 pyrin domain (PYD) was built

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

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

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

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

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

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

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

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

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

191 n the YpenMan26A structure was compared to a homology model of Wsp.Man26A from Westerdykella sp. and

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

193 Homology modeling of Aspergillus fumigatus DHODH has ide

194 Homology modeling of BjNRAMP4.1 suggested that it could

195 The CC4 structure, together with homology modeling of CC1, reveals the surface locations

196 Using homology modeling of ENaC structure and site-directed mu

197 Homology modeling of its major structural subunit, CotA,

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

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

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

201 The procedure includes homology modeling of the DARPin, modeling of the flexibl

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

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

204 Homology modeling of the modifying enzyme DpdA provides

205 Sequence comparison and structural homology modeling of the N-terminal domain of LtpM uncov

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

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

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

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

210 Here we carried out tertiary structure homology modelling of the peroxidases for docking studie

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

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

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

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

215 Homology models of hNTPDase1 and -2 were constructed.

216 by using an in silico approach, we built 3D homology models of human DNAJA1 and mutp53(R175H) protei

217 ociated with each conformation type, and for homology models of kinases in inactive conformations.

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

219 The server also allows users to upload homology models of microbial proteins.

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

221 sing compatibility of candidate molecules to homology models of sugar-binding site.

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

223 molecular modeling suite, we generated three homology models of the alpha (2) beta (3) gamma (2) rece

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

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

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

227 6 (TMD) was subsequently utilized in docking homology models of the ECD and the TMD to create a full-

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

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

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

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

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

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

234 computational tool that builds downloadable homology models of variable domain sequences, tests them

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

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

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

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

239 PfCPSF3 homology models placed these mutations in the active sit

240 Homology models predict that the ligand-binding pockets

241 d across SLC35 A subfamily members, and a 3D-homology model predicted that Glu-47 and Lys-50 are faci

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

243 L1 crystallographic homology models predicted a degree of structural diversi

244 Homology modeling predicts protein structures using know

245 Homology modeling predicts that contact between the enve

246 Structural homology modeling predicts that this protease adopts a f

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

248 tructural information for LPL was limited to homology models, presumably due to the propensity of LPL

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

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

251 Homology modeling revealed glutamyl and aspartyl residue

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

253 Sequence alignment and homology modeling showed distant homology between GP38 a

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

255 Structural analysis and protein homology modeling showed the presence of spontaneous mut

256 Homology modeling shows that the scramblase domain forms

257 Protein homology modeling studies showed significant structural

258 Homology modelling, substrate docking, molecular dynamic

259 Homology modeling suggested that the Glu-221 side chain

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

261 Homology modeling suggested that the primary V3 loop bnA

262 Homology modeling suggested that the structure of region

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

264 Molecular docking to AQP3, AQP7, and AQP9 homology models suggested interactions between these inh

265 Structural analysis based on the homology model suggests cation-pai interactions as the m

266 Homology modeling suggests that the Ebola virus polymera

267 Protein homology modelling suggests that four amino acid substit

268 Here, homology modeling supported the alternating access trans

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

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

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

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

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

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

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

276 ike agonist (E2) of the TSHR, and structural homology modeling to unravel the functional and structur

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

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

279 a hybrid approach, using biological data and homology modeling, to study chemokine-GPCR interactions.

280 onal methods, based on crystal structures or homology models, to identify effective sites for inserti

281 Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional struc

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

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

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

285 nal conservation in 4,715 proteins and 3,951 homology models using 860,292 missense and 465,886 synon

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

287 On the basis of a homology model we argue that this binding mode also appl

288 Via homology modelling we predicted and confirmed an integra

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

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

291 By homology modeling, we identified the corresponding L596-

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

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

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

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

296 9% among 31 HoTP structures obtained through homology modeling, while ZDOCK alone returns 14 and 3%,

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

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