ライフサイエンスコーパス: dock

1 thod, GIST, readily implemented in molecular docking.

2 er is a widely used tool for protein-protein docking.

3 an be mapped through noble gas diffusion and docking.

4 teps of vesicular release, including vesicle docking.

5 plementary constraints for in silico protein docking.

6 ld serve to increase the fidelity of vesicle docking.

7 reference agent was studied using molecular docking.

8 e-form on the synaptic vesicle to facilitate docking.

9 ow consisting of protein sampling and ligand docking.

10 physiology of cilium; terms associated with docking.

11 , we sought a broader range of chemotypes by docking 2.2 million fragments, which revealed another th

12 F)1 (ARHGEF1), and dedicator of cytokinesis (DOCK)2 GEFs mediate CXCL12-induced LFA-1 activation in h

13 en targets using bound monomer structures in docking, 35% (6/17) when using unbound, and 12% (2/17) w

14 Finally, we identify by molecular docking a binding site in the ion pore that we confirm b

15 holoenzyme assembly through primer-template docking, accelerate RPR evolution, and allow RPR-catalys

16 Ligands were predicted by docking against a comparative model based on a eukaryoti

17 tide fragment ensemble generation, the PIPER docking algorithm for exhaustive fragment-receptor rigid

18 The general usefulness of the docking algorithm was highlighted by redocking of peptid

19 -end in an ATP-like state, it does not fully dock along the motor domain.

20 Additionally, unbiased docking also showed Abeta binding at this site.

21 Expression and molecular docking analyses suggest involvement of specific members

22 T-box combined with molecular modelling and docking analyses suggest that the antibiotics that promo

23 transfection agents and proposes the use of docking analysis as a preliminary screening tool for the

24 Molecular docking analysis revealed two distinct binding sites wit

25 Results from docking analysis suggested that outward and outward-occl

26 a and FANCD2, which was confirmed by protein docking analysis.

27 ert liposomes into trafficking vesicles that dock and fuse with early endosomes, thus overriding the

28 Rho guanine nucleotide exchange factors Elmo/Dock and intersectin (ITSN).

29 that GPR124 promotes cell adhesion via Elmo-Dock and ITSN.

30 two agonists (compounds 3 and 17), out of 19 docked and synthesized compounds, that fit the receptor

31 quently, using binding assays, computational docking and cellular studies, we show that QseB interact

32 Through molecular docking and comparisons between the crystal structures o

33 n SNAP25 is a key player in synaptic vesicle docking and fusion and has been associated with multiple

34 a new platform for monitoring SNARE-mediated docking and fusion between giant unilamellar vesicles (G

35 llowing us to compare the process of vesicle docking and fusion on the supported parts of the PSMs (s

36 REs with only few milliseconds delay between docking and fusion.

37 Using a combination of in silico molecular docking and in vitro directed evolution in a well-charac

38 embrane cholesterol, facilitating Salmonella docking and invasion.

39 Mutational analysis coupled with molecular docking and molecular dynamics modeling revealed that MB

40 Using a combination of data-driven flexible docking and molecular dynamics simulations guided by pre

41 ection of reactive surfaces, protein-protein docking and molecular simulations, we found that two lar

42 Structure-activity relationship, docking and mutagenesis studies revealed the crucial int

43 Notably, DUck is orthogonal to docking and other 'thermodynamic' methods.

44 method for homology modeling and rigid-body docking and present the results for 1) the Antibody Mode

45 Unc13 proteins are required for vesicle docking and priming during exocytosis.

46 Optimal vesicle docking and priming is only possible when Munc13 heterod

47 osed distinctively different AZM mediated SV docking and priming models: sequential and concurrent SV

48 By molecular docking and receptor binding assays, we showed that c-CA

49 for exhaustive fragment-receptor rigid-body docking and Rosetta FlexPepDock for flexible full-atom r

50 with lysosomal vesicles that regulates their docking and secretion at the synaptic interface has not

51 tribute substantially to vesicle priming and docking and their loss reduces the readily releasable po

52 es on nucleotide- and substrate-controllable docking and undocking of its nucleotide-binding domain (

53 nal approach of binding site identification, docking, and interaction energy calculations to design a

54 catalytic core, creates a space for 3' exon docking, and restructures the pairing of the 5' splice s

55 The DOCK-AND-LOCK (DNL) method is a platform technology that

56 re freely available at github.com/Shamir-Lab/DOCKS/ and acgt.cs.tau.ac.il/docks/, respectively.

57 ental technique with a unique importance for docking approaches.

58 ble the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence de

59 om scoring functions used in protein-protein docking, as well as an energetic term considering the co

60 IP2) to make PI3Kalpha competent for bilayer docking, as well as for subsequent binding and phosphory

61 enous RNA tracking reveals that RNA granules dock at sites of branch emergence and invade stabilized

62 for releasing the viral genome from capsids docked at nuclear pores.

63 lysosomal vesicles, which are recruited and docked at the center of the immune synapse of B-cells.

64 ccurate and efficient global peptide-protein docking at high-resolution with remarkable accuracy, as

65 The study is the first structure-based cross-docking attempt aimed at distinguishing antibody-antigen

66 Cell surface connexons dock between adjacent cells to allow for gap junctional

67 NMR experiments demonstrate intramolecular docking between N- and C-terminal domains of PrP(C), rev

68 Docking (binding energy -8.124kcal/mol) and simulation s

69 , selective reduction of exocytosis of short-dock (but not no-dock) newcomer SGs accounted for the re

70 ffinity that can be triggered by the vesicle docking C2B-PIP2 interaction and raise the possibility t

71 Molecular docking calculations predict that UQ interacts with phen

72 Finally, molecular docking calculations provided further insights into how

73 nteraction is mediated by a conserved common docking (CD) domain within the carboxyl-terminal domains

74 sulting phosphorylation of Sid4 by the newly docked CK1delta recruits Chk2(Cds1) to Sid4.

75 124 also promotes the activation of the Elmo-Dock complex, as measured by Elmo phosphorylation on a c

76 On the basis of an iterative approach of docking, compound preparation, biological testing, and S

77 re the development and validation of the GAG-Dock computational method to predict accurately the bind

78 Induced fit docking computational simulations performed on the new s

79 NL initial segment (NIS) adopting a backward-docked conformation and the preceding alpha6 helix parti

80 tional ensemble and stabilization the domain-docked conformation in presence of ADP and ATP.

81 molecules of Prc and forms three-sided MepS-docking cradles using its tetratricopeptide repeats.

82 According to CAPRI peptide docking criteria, an acceptable conformation can often b

83 We demonstrated the importance of a MAPK docking domain necessary for protein-protein interaction

84 P18alpha, revealed that the dimerization and docking domain of RIIbeta is between its second cAMP bin

85 osphorylation within both the kinase and the docking domains and observed that lower concentrations o

86 tion sites can significantly affect the SV's docking efficiency and distribution of its contact area

87 0 mV) than the other clusters, and molecular docking experiments indicate that the physiological elec

88 se revealed plausible common scaffolds while docking experiments predicted binding poses and specific

89 NE aggregates of Nesprin1alpha and Sun2 that dock filaments of rootletin at the nuclear surface.

90 ion by a medicinal chemist, manual modeling, docking followed by manual filtering, and free energy ca

91 uctures confirmed binding modes predicted by docking for three scaffolds.

92 eading to these differences in signaling, we docked formoterol and clenbuterol to six structures of t

93 fluorescent signal enables detection of DCV docking, fusion-pore opening, and vesicle collapse into

94 of commercial chemical space using molecular docking gives access to fragment libraries that are seve

95 eal that a single point-site mutation at the docking hydrophobic patch of a Cu-azurin causes minor st

96 rt B holocomplex, from the large pool of pre-docked IFT-B complexes, and thus initiates ciliary entry

97 fungicides, all fungal P450 inhibitors, that dock in the catalytic site.

98 The domain structures were then docked in silico to provide a generic model for the NOX

99 cted mutated transporters, and computational docking in a BGT1 homology model based on the newly dete

100 Docking in silico of 121 pesticide contaminants of Ameri

101 thereby retarding SNARE assembly and vesicle docking in vitro.

102 y unresolved helix belonging to the R domain docked inside the intracellular vestibule, precluding ch

103 n microscopy, we have identified a subset of docked insulin granules in human beta cells and rat-deri

104 ls and an increase in the number of membrane-docked insulin secretory granules.

105 se two spatially distinct, individually weak docking interactions facilitate the highly specific reco

106 We hypothesized that these docking interactions sequester limiting amounts of DDK,

107 of the Fe protein has the most complementary docking interface with flavodoxin compared with the MgAT

108 e structure was computationally optimized to dock into MD-2 and CD14 binding sites.

109 tive, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme.

110 -like interaction that is critical for GW182 docking into one of hAgo1's tryptophan-binding pockets.

111 dation could in part be rationalized through docking into the previously disclosed 3-CRBN-GSPT1 cocry

112 k can overcome two fundamental challenges of docking large toxin peptides to ion channel homology mod

113 his prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecul

114 r, we focus on the exoskeletal growth of the dock leaf beetle Gastrophysa viridula, capturing all asp

115 DINC 2.0 allows docking ligands that were previously too challenging for

116 differing V gene segment usage and different docking mechanisms, mutational analyses showed that the

117 Zippering of SNARE complexes spanning docked membranes is essential for most intracellular fus

118 We use a Fast Fourier Transform (FFT) based docking method to quickly perform global rigid body dock

119 erimental results were compared to molecular docking method.

120 ergetic calculations to minimize loops, (ii) docking methodology to refine the VL-VH relative orienta

121 existing protein-protein and protein-peptide docking methods are not able to model them.

122 near-native structures when applied to four docking methods, resulting in a near-native appearing in

123 enine-based inhibitors using biochemical and docking methods.

124 led that the TRBV9(+) TCR adopts a different docking mode and molecular footprint atop HLA-E when com

125 The top-ranked docked model predicted that a region in the nucleotide-b

126 Additionally, we present a molecular docking model for how this active site can unhook either

127 rA/FtsK ATPase superfamily; (iv) a molecular docking model of the pentamer is compatible with the loc

128 k for flexible full-atom refinement of PIPER docked models, we successfully addressed the challenge o

129 Docking models and cross-linking patterns between the Fe

130 ition for the P-CR domain from the molecular docking models places the P-CR connector loop into a hyd

131 Although top-ranked docked molecules with and without the GIST term often ov

132 substrates are believed to require consensus docking motifs (D-site, F-site) to engage and facilitate

133 transcription factor Ets-1 has no canonical docking motifs, yet it is efficiently phosphorylated by

134 tion of exocytosis of short-dock (but not no-dock) newcomer SGs accounted for the reduced second-phas

135 Molecular docking of AhAI revealed tighter interactions with activ

136 ral (ret)Arl13b(-/-) photoreceptors revealed docking of basal bodies to cell membranes, but mature tr

137 Wnt-dependent docking of beta-catenin to the enhanceosome apparently c

138 Simulated docking of DCUK-OEt at the GABAA receptor suggested that

139 Molecular dynamics simulations following docking of each of the ligands into a model of the D3R d

140 Docking of exemplar antagonists from two chemical series

141 Computer-based docking of inhibitors to the NNMT substrate (nicotinamid

142 We thus turned to prospective docking of large libraries to investigate GIST's impact

143 cket extends into the dimeric interface, and docking of LDNF identified key residues for glycan inter

144 e protein structure database or by ab initio docking of monomer structures resolved by experiment or

145 NA-packaging proteins provide a scaffold for docking of multiple DNA repair factors, the absence of h

146 selective NTS2 ligands by investigating the docking of novel NT[8-13] compounds at both NTS1 and NTS

147 The individual contributions due to docking of the approximately 13-residue neck linker to t

148 de release of the capsid into the cytoplasm, docking of the capsid at a nuclear pore, and release of

149 The docking of the farnesyl group to the hydrophobic pockets

150 regulate this interaction in vivo Molecular docking of the L-selectin tail to mu1A was used to ident

151 We also show that docking of the sorting platform results in significant c

152 tural cassette exons by promoting productive docking of the spliceosomal U1 snRNP to a suboptimal 5'

153 method to quickly perform global rigid body docking of these fragments to the receptor.

154 positioning of the decorations might permit docking of xylan onto the hydrophilic face of a cellulos

155 eed from chaperones during acute stress, can dock on cellular membranes thus performing a proteostasi

156 n a second, SepD-coupled step, translocators docked on SepL become secreted.

157 ssemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate

158 t proteins required for cilia initiation and dock onto ciliary vesicles, but axonemal microtubules fa

159 on in the number of secretory granules (SGs) docked onto the plasma membrane (PM) at rest and reduced

160 t of the IDR was determined and subsequently docked onto the structure of the folded partner.

161 Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, posit

162 orm of preventive husbandry procedures (tail docking) or as a result of abnormal behaviour (tail biti

163 By incrementally docking overlapping fragments of a ligand, DINC allowed

164 otosystem II contact zones provide sites for docking phycobilisomes and the formation of megacomplexe

165 protein tripartite motif (TRIM)14 provides a docking platform for the assembly of the mitochondrial s

166 D CH1 region tyrosine motifs, which serve as docking platforms for signal transducers, such as Grb2.

167 We hypothesize that CI serves as a docking point for PD targeting and the intercellular mov

168 An analog that docked poorly in the GtfC catalytic domain failed to inh

169 Unique signatures are generated for each docking pose, allowing high-throughput ranking of whole

170 tion of near-native structures from a set of docked poses based on their calculable properties.

171 If a substantial number of low energy docked poses cluster in a narrow vicinity of the native

172 In contrast, if the interaction sites in the docked poses do not form a large enough cluster around t

173 was screened against the target focusing on docking poses with the core structure resembling a known

174 Our docking predictions correlated well with the cis-favored

175 erved a considerable increase in our protein docking predictions.

176 xocytosis in the final stages (including the docking, priming and fusion of granules) are poorly unde

177 odimer is an active component of the vesicle docking, priming and release complex.

178 priming models: sequential and concurrent SV docking/priming.

179 distances is generated which then drives the docking process and enables the determination of the cor

180 d protein (C11orf84), which we renamed SPIN1 docking protein (SPIN.DOC), that directly binds SPIN1 an

181 tein 2-associated binding protein 2 (Gab2)-a docking protein-governs the development of fatty liver d

182 DOCK proteins are guanine nucleotide exchange factors fo

183 ation of genes encoding for integrins and FA docking proteins.

184 have developed a robust NMR restraint guided docking protocol to generate high-quality models of prot

185 agment based high-resolution peptide-protein docking protocol.

186 atalytic activity and does not involve known docking recruitment sites on ERK2, and we obtain an esti

187 We validate that GAG-Dock reproduces accurately (<1-A rmsd) the crystal struc

188 lleviate model uncertainty, antibody-antigen docking resamples CDR loop conformations and can use mul

189 .com/Shamir-Lab/DOCKS/ and acgt.cs.tau.ac.il/docks/, respectively.

190 Protein-protein docking results also support Psb28 binding in this regio

191 and are in general agreement with molecular docking results.

192 de novo beta-actin hotspots colocalize with docked RNA granules at the bases and tips of new branche

193 sity of the models using RosettaDock's local dock routine lowers the discrimination accuracy with the

194 To release the stable docked SBP from the transporter hydrolysis of ATP is req

195 further investigation because of 1) its best docking score and 2) its binding capability at interacti

196 orrelation between ligand-enzyme interaction docking scores and experimentally calculated IC50 values

197 n silico studies, molecules with significant docking scores containing different derivatives of l-vas

198 Docking screening was performed through identified poten

199 ove the hit rates and ligand geometries from docking screens, although the magnitude of its effects c

200 more, in silico data, based on the molecular docking simulation, showed that GPAGPRGPAG, AVVPPSDKM, T

201 d sequence, phylogeny, homology modeling and docking simulation.

202 Molecular docking simulations and DNA footprinting experiments sug

203 rane fractions, was shown to bind to CD38 in docking simulations and reduced the isoproterenol-induce

204 e, allowing high-throughput ranking of whole docking simulations by pairwise comparison to experiment

205 tein subunit of microtubules, with molecular docking simulations, quantum chemistry calculations, and

206 a diprolyl chemical series was modeled using docking simulations.

207 The coiled-coil is a docking site for sigma factors on RNA polymerase, and ev

208 However, both residues lie within the final docking site for the protease in the antithrombin-protea

209 as a conformational switch that creates the docking site for the tail nozzle only after the assembly

210 posed to concertedly function as the primary docking site for twin-arginine signal peptides.

211 ons with the SBD, and the predominant linker-docking site is available in only one allosteric state,

212 small molecules that target the ED substrate-docking site may exert anti-inflammatory effects similar

213 was adjacent to but not overlapping with the docking site of an auto-regulatory motif, AutoN, in the

214 p38alpha glutamate-aspartate (ED) substrate-docking site rather than the catalytic site, the sequenc

215 Using the Mcl-1 BH1 domain as a docking site, we identified a small molecule, MI-223, th

216 e deduced from crystal structures, molecular docking, site-directed mutagenesis, and kinetic and ther

217 es in the transmembrane helices and effector docking sites at the intracellular surface of the beta1A

218 1, NPP-4, and NPP-11 primed at multiple Polo-docking sites by Cdk1 and PLK-1 itself physically intera

219 Acetyl-lysine modifications create docking sites for bromodomains, which are structurally c

220 DDK associates with docking sites on loaded Mcm double hexamers at unfired r

221 lacks specificity for substrates with cyclin-docking sites.

222 We used both in silico docking software, and in vitro molecular and biochemical

223 t of binding of 12 as predicted by the Glide docking software.

224 ognition of the viral MHC-I mimic UL18 and a docking strategy that relies on contacts with HLA-F as w

225 on, our group has previously proposed a meta-docking strategy, called DINC, to predict binding modes

226 eractions employing an exhaustive all-to-all docking strategy.

227 The backward-docked structure of NIS is essential for motility of the

228 s of highly populated clusters of low-energy docked structures.

229 ibitors (X I(50) values 0.00007-0.00008) and docking studies aid in understanding this selectivity.

230 Docking studies at hAR structures were performed to rati

231 More, molecular docking studies confirm that psiRGDechi recognizes the r

232 genesis combined with in silico modeling and docking studies for the first time offers experimental p

233 Docking studies have explained differential activities o

234 Both binding affinity assays and docking studies of the CYP121A1 inhibitors suggest type

235 Docking studies rationalized the results obtained in the

236 Molecular docking studies revealed a mechanistic model for the int

237 Docking studies revealed binding to the basic surface po

238 Docking studies suggest that the lack of the para-methox

239 Docking studies suggest that UBP684 binds to the GluN1 a

240 Western blotting and molecular docking studies suggested that these compounds bind effi

241 We performed docking studies to understand the interactions of compou

242 Docking studies using available crystal structures have

243 A receptor homology model was built and docking studies were performed to analyze ligand-recepto

244 oduction in Raw 264.7 macrophages, molecular docking studies were performed to provide insights into

245 Docking studies were performed with the synthesized comp

246 Docking studies were performed, and receptor mutants wer

247 ase but, in contrast to the predictions from docking studies, none bind strongly to this enzyme.

248 , which, along with crystal interactions and docking studies, suggests possible models for the partic

249 ailed kinetic characterization and in silico docking studies, we found that replacing this single ami

250 ar orientations as demonstrated by molecular docking studies.

251 he GPVI receptor have been explained through docking studies.

252 vity analysis, in combination with molecular docking studies.

253 A docking study of the benzoxepin ligands was undertaken.

254 A docking study revealed some critical sites for ATP bindi

255 resent a computational structure-based cross-docking study to test the identification of native antib

256 Molecular docking study was carried out on the analogs and referen

257 Protein docking supported by evolutionary restraints and machine

258 e report a virtual screen based on molecular docking that allows the affinity maturation of macrocycl

259 ody from sequence (RosettaAntibody) and then docking the antibody to protein antigens (SnugDock).

260 Docking the model of the FlgK junction onto the structur

261 en crystallographic and biological dimers by docking the two subunits to exhaustively sample the inte

262 anges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transfer

263 a conformation competent for 3'-splice site docking, thereby promoting exon ligation.

264 clustering and synaptic vesicle priming and docking through interactions with Munc13 and RAB3A, resp

265 solic stress granules, where nuclear factors dock to compensate RNA pathology.

266 te binding proteins (GBPs), which themselves dock to PVs through poorly characterized mechanisms.

267 ow that recombinant rootletin filaments also dock to the NE through the specific recruitment of an ap

268 In the current study we found that DCs docked to the basolateral surface of lymphatic vessels a

269 the s-PSM were fully immobile, whereas those docked to the f-PSM were mobile with a mean diffusion co

270 Our results demonstrate that vesicles docked to the s-PSM were fully immobile, whereas those d

271 the 35-amino acid NTR of MYO1C(35) (NTR(35)) docked to the X-ray structure of MYO1C(C), we predicted

272 ular dynamics simulations, and computational docking to analyze GRK5 interaction with the beta2-adren

273 In this study we evaluated in silico docking to develop MMP-subtype-selective tumor-activated

274 We used molecular docking to model the interaction of Hsp90Ec and DnaK.

275 demonstration of applicability of molecular docking to show both enantioselective electrochemical an

276 (Sec4), the extended coiled-coil tail blocks docking to the plasma membrane.

277 ould potentially prevent RNA polymerase from docking to the ribosome.Under conditions of nutrient lim

278 We develop a heuristic called DOCKS to find a compact UHS, which works in two phases:

279 on by HmuUV-T where the substrate-loaded SBP docks to the nucleotide-free outward-facing conformation

280 Docking tools are largely used for virtual screening of

281 tform submotif precedes the formation of the docking transition state and tertiary A-minor hydrogen b

282 or hydrogen bond interactions form after the docking transition state.

283 ents prior to and after the formation of the docking transition state.

284 complex into the peroxisomal membrane at the docking/translocation module (DTM).

285 We demonstrate the potential of the docking-undocking combination in a fragment screening ag

286 In particular, DOCKS uses less than 30% of the 10-mers needed to span t

287 tin-2 indicated that the receptor and ligand dock using the same molecular surface and a conserved "l

288 f simple shape-based algorithms and fragment docking using GOLD.

289 les contacting the dense projection and more docked vesicles at the plasma membrane.

290 re also characterized by a higher density of docked vesicles, suggesting that a concerted action of t

291 A computational study by molecular docking was made to complement the structural study.

292 ture-guided pharmacophore design followed by docking, we found two agonists (compounds 3 and 17), out

293 Using homology modeling followed by docking, we identified key protein residues in the KL1 d

294 ty acid (but not cholesterol) hydroperoxides docked well into the active site of Ohr from Xylella fas

295 ble binding modes obtained through in silico docking, which provide insights into the structural basi

296 hese findings were rationalized by molecular docking, which recognized interaction of phosphonic and

297 Consensus docking with an extended series of PAMs with chemical si

298 Docking with each energy parameter set results in ten mo

299 Docking with these structures can explain several minor

300 We show that DOCKS works well in practice and produces UHSs that are