ライフサイエンスコーパス: docking

1 represent a higher-level scoring theory than docking.

2 ss-linking, mass spectrometry, and molecular docking.

3 (ETD), chemical cross-linking, and molecular docking.

4 erformance and robustness of flexible ligand docking.

5 supported by molecular dynamics and ensemble docking.

6 ferent fatty acids and urethane by molecular docking.

7 ted methods exist for protein-small molecule docking.

8 the interacting membrane patches upon tight docking.

9 uman pathogenic mutations and toxic antibody docking.

10 ing Giardia's cell shape and guiding axoneme docking.

11 Three different ligand-docking algorithms (RosettaLigand, Glide, and Swissdock)

12 interactions were determined using molecular docking analyses.

13 sequence; (ii) an in silico peptide-protein docking analysis and in vitro binding assay that identif

14 Molecular docking analysis shows that C3G binds to the interface o

15 ratory conditions was not noticed, in silico docking analysis supports allosteric binding to glutamat

16 By computational docking analysis, biochemical assays, and advanced live-

17 ether with binding energies measurements and docking analysis, pointed out pelargonidin 3-robinobiosi

18 The docking and atomic scale fitting showed multiple discret

19 Docking and binding experiments suggest that Phe31 of EL

20 rom the active site, followed by active-site docking and bond cleavage.

21 rectifier K(+) channel AKT1 regulates kinase docking and channel activation.

22 osetta software for macromolecular modeling, docking and design is extensively used in laboratories w

23 hyaluronan receptor 1 (LYVE-1) mediates the docking and entry of dendritic cells to lymphatic vessel

24 ronavirus ACE-2, DPP4, or CD13 receptors for docking and entry.

25 ongly disrupted insulin and glucagon granule docking and exocytosis.

26 Furthermore, molecular docking and functional assays reveal key factors that ma

27 -4,5-P(2) ) is critical for synaptic vesicle docking and fusion and generation of the second messenge

28 displaying variations in motility as well as docking and fusion capability.

29 eractions with other elements of the vesicle docking and fusion machinery.

30 d target membrane fusion involves tethering, docking and fusion.

31 ing vesicle membrane tethering, facilitating docking and fusion.

32 he therapeutic target of Rg3 using molecular docking and gene silencing.

33 Docking and isothermal calorimetry titration confirmed i

34 s on target proteins were investigated using docking and molecular dynamics calculations.

35 Molecular docking and molecular dynamics simulation were performed

36 ith the extracellular loops, predicted using docking and molecular dynamics simulation with newly con

37 Protein-protein docking and molecular dynamics simulations provided mode

38 orter assays, chromatin immunoprecipitation, docking and molecular dynamics simulations, human unfold

39 Aided by computational docking and peptide screening, we identified a TTR segme

40 (2+) channels and activates synaptic vesicle docking and priming via Munc13-1.

41 both RIM and Munc13 mediate synaptic vesicle docking and priming.

42 analyses of fluorescence spectra, molecular docking and quantum-chemical calculations at DFT level.

43 Molecular docking and quantum-chemical calculations were consisten

44 meric lattice-structured platform for capsid docking and recruit viral and cellular NEC-associated fa

45 and X-ray scattering data with comprehensive docking and refinement revealed how XPA DBD and RPA70AB

46 studies establish a high-resolution channel-docking and resting-state locking mechanism for huwentox

47 Here, the constructed structural models, docking and scoring schemes were validated by their abil

48 Molecular docking and simulation predict the TDZD-8 binding confor

49 tudy demonstrates that refined computational docking and simulation studies combined with experiments

50 Together with computational docking and simulation, the structure suggests a molecul

51 ation of state-of-the-art tools in molecular docking and simulations, including an in-house simulatio

52 Using in silico docking and site-directed mutagenesis, we identified Asp

53 orthosteric binding site by using molecular docking and structure-based drug design to optimize liga

54 tration with immunocastration, avoiding tail docking and teeth clipping, and providing environmental

55 to the MHC-I T-cell epitopes using molecular docking and the complexes were relaxed with molecular dy

56 mber of tethering SNARE complexes upon loose docking and the size of the interacting membrane patches

57 ftware packages can simulate flexible ligand docking, and among them, Autodock is widely used.

58 nucleotide-dependent lid closing, N-M domain docking, and ATPase.

59 analysis, bio-kinetics simulation, molecular docking, and dynamics studies were performed for the sel

60 matics-based structure modelling, Cu(2+) ion docking, and MD simulations of peptide-MBP chimeras corr

61 logical profiles, including rate of killing, docking, and molecular dynamics studies, suggest that ou

62 SD17B10 was further evaluated using molecule docking, and results showed that MEHP has higher affinit

63 Kinetic, molecular docking, and site-directed mutagenesis analyses confirme

64 f the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional intera

65 , synapse and active zone structure, vesicle docking, and transsynaptic nano-organization were unimpa

66 ompare favorably with other state-of-the-art docking- and ligand-based methods, including AutoDock Vi

67 Whereas intramolecular MIDAS docking appears to require a treatment with a chemical i

68 4E cap binding site, we developed a covalent docking approach focused on lysine.

69 tudy, we applied a structure-based molecular-docking approach to find small molecules that specifical

70 PRI score set generated by a wide variety of docking approaches (i.e. docking software-non-specific).

71 ere, we used Rosetta structural modeling and docking as well as molecular dynamics simulations to stu

72 cific scaffolds for simulated small molecule docking (AutoDock Vina (Trott and Olson, J Comput Chem 3

73 assification model) and structure (molecular docking) based for identifying possible sweeteners from

74 Cross-validated using the protein-protein docking benchmark version 5.0, our method (ZING) achieve

75 We show that CDK enforces Spc72 asymmetric docking by phosphorylating Nud1/centriolin.

76 Molecular docking calculations confirm the proposed mechanism for

77 Molecular docking calculations further reveal that cholesterol reg

78 The docking calculations take place on the user's own comput

79 e orexin receptor subtype 2 in computational docking calculations with the aim to identify additional

80 surements, NMR titrations, and computational docking calculations, as well as biological investigatio

81 as modeled and confirmed by spectroscopy and docking calculations.

82 in functions and facilitates protein-protein docking calculations.

83 in cargo trafficking pathways by sorting and docking cargos for translocon-mediated transport across

84 We examined substrate binding by docking chlorothalonil (2,4,5,6-tetrachloroisophtalonitr

85 n the recent rounds of blind protein-protein docking competition CAPRI (Critical Assessment of Predic

86 n of the major components of the peroxisomal docking complex Pex14p/Pex17p, in a native bilayer envir

87 In silico docking confirmed the ability of 5a-5g to bind to the ac

88 rogress, reliably distinguishing near-native docking conformations from a large number of candidate c

89 SO in finding both low-energy and small-RMSD docking conformations with high robustness in most cases

90 ict the general position of the Dimerization/Docking (D/D) domain, which is essential for localizatio

91 l titration nanocalorimetry (ITC), molecular docking (DC), and molecular dynamics (MD) were used to c

92 nal deep neural network-based approach named DOcking decoy selection with Voxel-based deep neural nEt

93 covery of protein-protein and protein-ligand docking discrimination tests.

94 or or preribosome binding, bimolecular MIDAS docking does not.

95 In this study, the module docking domain (DD) affinity prediction performance on a

96 N- and C-terminal docking domains are usually responsible for mediating th

97 ring a comprehensive annotation of available docking domains information in bacterial biosynthetic pa

98 , and associated the histidine substrate and docking domains with the kinase core, thus preventing ca

99 o molecular docking using Bristol University Docking Engine to screen a library of more than 8 millio

100 ical peptide region that engages a substrate docking exosite and a C-terminal transition-state analog

101 cement experiments demonstrate that both the docking exosite and the active site are engaged by the b

102 native structural conformations from protein docking experiments and outperform other contact-based p

103 esults of the steered molecular dynamics and docking experiments indicated that the canonical PLB-bin

104 ecular dynamics and membrane protein-protein docking experiments to achieve both a global search and

105 immunofluorescence, molecular modeling, and docking experiments to characterize the mechanisms drivi

106 he saccharide core of PG using computational docking experiments, and multiangle light-scattering exp

107 ther probed and rationalised using molecular docking experiments, which indicated that conjugated hal

108 Protein-ligand docking has emerged as a particularly important tool in

109 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D str

110 of Opa1 (l-Opa1) is sufficient for membrane docking, hemifusion and low levels of content release.

111 lecule library to performing and visualizing docking in a few clicks.

112 Br-PBTC-binding site through mutagenesis and docking in alpha4.

113 is a reliable choice for the flexible ligand docking in Autodock software.

114 he isoproterenol-induced increase in vesicle docking in cerebellar slices.

115 erves to prevent, rather than promote, MIDAS docking in the absence of inducing signals.

116 heterogeneity that resulted in variations in docking interactions.

117 N-terminus masks the [4Fe-4S] cluster at the docking interface between BchL and BchNB.

118 release of the flexible N-terminus from the docking interface.

119 o position the CXCL12 N terminus for optimal docking into the orthosteric pocket of CXCR4 and suggest

120 Docking into the two receptor structures recently determ

121 Molecular docking is a computational technique for predicting how

122 design and development, and flexible ligand docking is a widely used method for docking simulations.

123 nd fully replenish the docked pool, but this docking is transient and they either undock or fuse with

124 Here, molecular docking is used to detect specific binding sites ("hot s

125 Upon chromatin docking, KAP1 first associates with RNA Pol II and then

126 ions is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, po

127 t proceeds through distinct steps, including docking, merger of proximal leaflets (stalk formation),

128 1-thin filament models by employing unbiased docking methodologies, which test billions of trial rota

129 icted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope

130 ishing the subsequent alphabetaTCR canonical docking mode.

131 r modeling study, based on a receptor-driven docking model and including a systematic free energy per

132 Finally, a molecular docking model was used to rationalize the selective bind

133 To evaluate a protein docking model, DOVE scans the protein-protein interface

134 Using a computer docking model, we identified a novel dual-target inhibit

135 for furan compounds, supported by in silico docking modeling.

136 earning models were trained and validated on docking models available in the ZDock and DockGround dat

137 neural nEtwork (DOVE) for evaluating protein docking models.

138 n vitro immuno-infrared sensor measurements, docking, molecular dynamics simulations, and ab initio c

139 Here, we use a combination of ligand docking, molecular dynamics simulations, and electrophys

140 we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molec

141 Finally, we find that variation in docking motif potency can advance or delay the time at w

142 rovide a general method for surveying viable docking motif sequences and quantifying their potency in

143 assay to comprehensively characterize the LP docking motif, which determines G1-CDK substrate specifi

144 yeast, CDK substrates with Leu/Pro-rich (LP) docking motifs are recognized by Cln1/2 cyclins in late

145 ng eukaryotic cell division, cyclin-specific docking motifs help cyclin-dependent kinases (CDKs) phos

146 fying enzymes recognize their substrates via docking motifs, but the range of functionally permissibl

147 Using molecular docking, nuclear magnetic resonance, lipid-binding assay

148 In silico docking of 2,3,5,6TMP-TQS in the putative allosteric act

149 Two iterative rounds of docking of a carefully selected set of natural-product-d

150 Based on docking of a nuclear localisation sequence, point mutati

151 Molecular docking of a series of compounds including amiodarone, a

152 Molecular docking of analogues that retained antiviral activity de

153 Docking of ATP on a structure of E. coli DnaA, modeled u

154 Here, we identify the docking of CaN to the gamma isoform of MKK7, a component

155 p98-Rae1 via its C-terminal domain to impair docking of cargo-receptor (karyopherin/importin) complex

156 Its activity is temporally regulated by the docking of different activating subunits, known in plant

157 ze the biological effect of GK-15, molecular docking of GK-15 into the N-terminal extracellular ligan

158 the epitaxial growth is enhanced by lateral docking of hBN to Cu (111) steps, ensuring the mono-orie

159 mpact structure than that predicted from the docking of homologous crystal structures of the separate

160 In silico docking of indole on DNA gyrase predicts that indole doc

161 ides selective recognition and high-affinity docking of large dense core secretory vesicles to the pl

162 ADAM22/23-docked LGI1, but all inhibited the docking of LGI1 to ADAM22/23.

163 ne cassettes is proposed, based on molecular docking of plant metabolites within the ATP and D-cyclos

164 substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of S

165 Granuphilin is involved in membrane docking of secretory vesicles.

166 , we present an algorithm for template-based docking of small molecules.

167 release at the presynaptic terminal requires docking of synaptic vesicles to the active zone membrane

168 Docking of the compounds into the HLA-DRB1*15:01 and HLA

169 Computer docking of the methylnicotines to the Lymnaea acetylchol

170 Recent models suggest that intramolecular docking of the MIDAS domain onto the AAA ring is require

171 Docking of the tetraspanin 33 C terminus revealed that i

172 Further, molecular docking of these molecules on sweet taste receptor perfo

173 n together with atomic scale protein-protein docking of tropomyosin to the EM models.

174 rays of intercellular channels formed by the docking of two hemichannels from adjacent cells.

175 ion to light-dependent activation, "envelope docking" of ACCase permits fine-tuning of fatty acid sup

176 osed that different S-components compete for docking onto the same ECF module, but a minimal liposome

177 ster molecules by similarity and personalize docking parameters.

178 ous sites: adenosine at the ATP-pocket and a docking peptide (PIFtide) at the PIF-pocket, on a model

179 the closest ideal Cn symmetric complex from docking poses containing a homo-dimer without prior know

180 "Horizontal" docking precludes germline CDR1beta- and CDR2beta-MHC bi

181 In fact, molecular docking predicted a high affinity of CGA for alpha-gluco

182 Computational protein-protein docking predicted that p.P888L SAP97 is more likely to f

183 In silico docking predicted the active ligands interacted with gly

184 ith the OX1R and corresponded closely to the docking-predicted geometry.

185 hen searches for templates and uses them for docking, presenting the user with top-scoring poses and

186 ness in solving both holo- and apo-structure docking problems with different numbers of torsions, whi

187 The docking programs PIPER and ClusPro were used, followed b

188 Among docking programs, AutoDock Vina is particularly popular.

189 Like many docking programs, Vina requires users to download/instal

190 s able to use a variety of the most powerful docking programs.

191 the cargo-loaded receptor interacts with the docking protein Pex14p that is tightly associated with P

192 ions, including an in-house simulation-based docking protocol, to investigate the binding properties

193 To date, several molecular-docking protocols have been employed to identify troponi

194 re, we combine computational methods (ligand docking, quantum mechanics/molecular mechanics optimizat

195 Here, we investigate the substrate-docking region, the hydrophobic patch, on the fission ye

196 This in vitro evidence was corroborated by docking results demonstrating favorable interactions bet

197 The docking results did not match the known pose and affinit

198 rther structural analyses with computational docking results uncover the differences between CB2 and

199 Inhibition was also showed by the in silico docking results which show that lutein interacted with t

200 Based on their docking scores, top three molecules (Barrigenol, Kaempfe

201 Molecular docking screens against crystal structures of the A(2A)

202 anuphilin, is a Rab effector responsible for docking secretory vesicles to the plasma membrane before

203 In silico docking showed that 3-O-acetylation of the upstream resi

204 Molecular docking showed that C-B or C-I binds to the ankyrin doma

205 substances with hTRPV1 analyzed by molecular docking simulation also displayed the same law.

206 Additionally, a molecular docking simulation has been carried out using the HIV-1

207 s using photoactivable anesthetics and rigid docking simulation showed that isoflurane and sevofluran

208 Molecular docking simulation suggested that DPP6-L may associate w

209 were strategically redesigned by performing docking simulation, following surface-electrostatic pote

210 d to be located in the trimeric interface by docking simulation.

211 Docking simulations on the M(3) mAChR-resolved structure

212 Computational docking simulations predict a greater binding affinity t

213 rinsic fluorescence studies, and induced fit docking simulations provided a mechanistic understanding

214 Using molecular docking simulations we compared the SARS-CoV and SARS-Co

215 oviding strong insights to improve molecular docking simulations, especially regarding the interactio

216 An in silico structural approach based on docking simulations, pharmacophore modeling and molecula

217 We combined and integrated docking simulations, with molecular dynamics (MD), Super

218 s, native mass spectrometry (MS), and ligand-docking simulations.

219 e ligand docking is a widely used method for docking simulations.

220 ormational homology modeling associated with docking simulations.

221 ons between the LC3-interacting region (LIR) docking site (LDS) in ATG8s and LIR motifs in various in

222 ex formation with LegK7 but also served as a docking site for downstream substrates such as the trans

223 in 153 (Nup153), which is known to provide a docking site for protein-cargo complexes at the nuclear

224 ation of CD5 tyrosine 429, which serves as a docking site for proteins with adaptor functions (c-Cbl,

225 stone H3 at threonine-3 (H3T3ph), creating a docking site for the Chromosomal Passenger Complex (CPC)

226 ecular-level characterization identified the docking site on PrP(C) that underlies the stereoselectiv

227 sed to pattern RhoA activation by creating a docking site on the central spindle that concentrates th

228 viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively g

229 rsible tPAINT probe that exposes its cryptic docking site permanently and thus integrates force histo

230 engineered reversible probes with a cryptic docking site revealed only when the probe experiences fo

231 ination of homology protein modeling, ligand docking, site-directed mutagenesis, and electrophysiolog

232 pPAINT uses a split-docking-site configuration to detect spatial proximity w

233 minal structure suggested the existence of 2 docking sites for PC1 within the N terminus of Kv4.3, su

234 plasma membrane through dephosphorylation of docking sites on the receptors.

235 Nuclear Pore complexes (NPCs) act as docking sites to anchor particular DNA lesions facilitat

236 of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST deca

237 ic1, contains linear phosphorylation motifs, docking sites, and phosphodegrons to empower an N-to-C t

238 Many docking software packages can simulate flexible ligand d

239 y a wide variety of docking approaches (i.e. docking software-non-specific).

240 g functions on two independent datasets: (i) Docking software-specific models and (ii) the CAPRI scor

241 the docking strand, and a spacer between the docking strand and the affinity agent.

242 the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand

243 2.2 and DQ2.2-glut-L1 (PFSEQEQPV) revealed a docking strategy, and associated interatomic contacts, w

244 y in vivo, and they reveal how variations in docking strength can tune the degree and timing of regul

245 The authors show that LP-cyclin docking strength determines the timing of Sic1 degradati

246 as blueprint, backed-up by automated ligand docking, structure-guided mutagenesis of OC43, BCoV, and

247 zyme, protein mass spectrometry analysis and docking studies allowed us to gain an insight into the i

248 In vitro and molecular docking studies attributed the non-competitive character

249 Structure-guided mutagenesis and docking studies demonstrate the interactions of MaDA wit

250 Molecular docking studies have highlighted that quercetin, a natur

251 Supporting the experimental results, docking studies have revealed that danazol can likely bi

252 Specifically, molecular docking studies identified patterns driving affinity and

253 Computational docking studies illustrate the observed activity differe

254 Detailed docking studies of a potent difluorinated probe with MMP

255 Docking studies on the bacterial sugar transporter vSGLT

256 logy model of GPR84 was generated to perform docking studies rationalizing the experimental data.

257 Docking studies revealed stable interactions of the vacc

258 Docking studies revealed that the scFv recognizes an epi

259 Docking studies showed that compound 5 did not reach hig

260 Docking studies suggest a heparin/heparan sulfate-bindin

261 Competition and molecular docking studies suggest that BHC and blebbistatin bind t

262 In silico docking studies were undertaken to assess the predicted

263 From molecular docking studies, the relative binding energies of the em

264 actions between drug and HSA using molecular docking studies.

265 ith pepstatin and screened through molecular docking studies.

266 logical temperatures for aiding in molecular docking studies.

267 Docking study and biological evaluation of synthesized c

268 fonate (TNS) and validated using a molecular docking study with AutoDock Vina.

269 1) in silico, where modeling ligand-protein docking suggested that 6-OH-BDE-47 is a promiscuous ATP-

270 Molecular docking suggested that a hydrophilic region, primarily m

271 er structures generated by NMR-based protein docking, suggesting that the ASC dimer could be a basic

272 Computational docking suggests hydrophobic residues in the pocket are

273 Additionally, in silico molecular docking suggests that Abeta can bind favorably to Cx43.

274 mechanistic insight, combined with simulated docking techniques, allows for the design and optimizati

275 The docking tests indicated that the Trp containing peptides

276 Docking them into an 11.4- angstrom-resolution cryoelect

277 tropomyosin or actin-tropomyosin yet avoided docking TnT domains that lack known or predicted structu

278 roximal effects of GLUT4-containing vesicles docking to and fusion with the PM, also directly regulat

279 Molecular docking to AQP3, AQP7, and AQP9 homology models suggeste

280 We performed computational docking to generate a structural model of m102.4-NiV int

281 on-demand" virtual library, we used covalent docking to identify arylsulfonyl fluorides that target a

282 king mass spectrometry (XL-MS) and molecular docking to interrogate the three-dimensional architectur

283 .9 angstrom resolution which allows us using docking to suggest a mechanism of interaction between co

284 the same conserved rRNA tertiary surface for docking to the 30S.

285 mechanism of its interference with the virus docking to the host cell receptor.

286 This results in erroneous, lateral centriole docking to the nucleus, leading to spermatid decapitatio

287 c mechanism that ensures proper proximal end docking to the nucleus.

288 o the plasma membrane and their anchoring or docking to the plasma membrane (PM).

289 However, PLK-2 docking to the SC is prevented by the nucleoplasmic HAL-

290 , we first employed unbiased protein-protein docking tools to identify binding specificity of individ

291 d that of the TRAV1-2(+) and TRAV36(+) TCRs' docking topologies on MR1.

292 Here, we use in silico molecular docking using Bristol University Docking Engine to scree

293 Computational docking, validated by mutagenesis and kinetic studies, i

294 Molecular docking was carried out to investigate alpha-glucosidase

295 Here, computational protein-protein docking was used to delineate a Vif/CBF-beta/PPP2R5 comp

296 Docking was used to explore the active site of the out c

297 recently, a new predictive method, reactive docking, was developed, building on the growing corpus o

298 l assays, structural modeling, and molecular docking, we demonstrate that Endosidin20 (ES20) targets

299 s as distance restraints for protein-protein docking, we generated a high-confidence model of the IL-

300 s (OTIs), designed by molecular modeling and docking, were synthesized.