ライフサイエンスコーパス: docking

1 an be mapped through noble gas diffusion and docking.

2 teps of vesicular release, including vesicle docking.

3 ld serve to increase the fidelity of vesicle docking.

4 plementary constraints for in silico protein docking.

5 reference agent was studied using molecular docking.

6 g of biophysical data to drive computational docking.

7 eling and 250 CPU-hours for antibody-antigen 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 thod, GIST, readily implemented in molecular docking.

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

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

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

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

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

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

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

19 Our approach employs a fast docking algorithm to find shape complementary ligand pla

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

21 We developed a docking algorithm, ToxDock, which used ensemble-docking

22 des using secondary structure prediction and docking algorithms suggest that this hairpin interaction

23 We present a novel algorithm, Memdock, for docking alpha-helical membrane proteins which takes into

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

25 Expression and molecular docking analyses suggest involvement of specific members

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

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

28 Molecular docking analysis revealed two distinct binding sites wit

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

30 In silico docking analysis, competition binding experiments, and d

31 alysis, structural superimposition, RSMD and docking analysis, the possible structural-functional rel

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

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

34 Through molecular docking and comparisons between the crystal structures o

35 peptides are barriers to their computational docking and design.

36 king algorithm, ToxDock, which used ensemble-docking and extensive conformational sampling to dock al

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

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

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

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

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

42 In conclusion, by combining docking and in vitro HTS, competitive and noncompetitive

43 embrane cholesterol, facilitating Salmonella docking and invasion.

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

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

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

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

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

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

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

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

52 dels we develop a stochastic AZM mediated SV docking and priming model.

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

54 mitter release, playing key roles in vesicle docking and priming.

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

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

57 veloped a new methodology for protein-ligand docking and scoring, WScore, incorporating a flexible de

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

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

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

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

62 Crystal structure, substrate docking, and mutagenesis experiments have identified a c

63 Homology modeling of YdgR, Cam docking, and mutational studies suggested a binding mode

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

65 ental technique with a unique importance for docking approaches.

66 stituents that usually complicate the use of docking approaches.

67 sideration the lipid bilayer environment for docking as well as for refining and ranking the docking

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

69 al structure, kinetic experiments, molecular docking, as well as expression patterns of PviPRX9 acros

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

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

72 ed fast synaptic vesicle release and vesicle docking at the active zone independent of CaV2.1 abundan

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

74 3 as necessary and sufficient for basal body docking, axonemal extension, and motility during the dif

75 A pharmacophore and docking-based virtual screening of compound libraries le

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

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

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

79 In addition, docking calculations around the observed binding site fo

80 Molecular docking calculations predict that UQ interacts with phen

81 Finally, molecular docking calculations provided further insights into how

82 ns simulation and were used for an ensemble docking campaign.

83 growing body of research shows that protein docking can, in principle, be used to predict biological

84 king as well as for refining and ranking the docking candidates.

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

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

87 Induced fit docking computational simulations performed on the new s

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

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

90 Molecular docking demonstrated a hydrophobic binding pocket for th

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

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

93 Cys-162 of p38alpha, close to the known MKK3 docking domain, were relevant for these redox characteri

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

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

96 0 mV) than the other clusters, and molecular docking experiments indicate that the physiological elec

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

98 Structural docking experiments revealed that the epsilon ring of lu

99 Molecular docking experiments suggest potential TLR2 binding modes

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

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

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

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

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

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

106 Docking in silico of 121 pesticide contaminants of Ameri

107 thereby retarding SNARE assembly and vesicle docking in vitro.

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

109 s-1 and involves two suboptimal noncanonical docking interactions instead of a single canonical docki

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

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

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

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

114 Molecular docking is a standard computational approach to predict

115 MPK (hTMPK) inhibitor YMU1 (1a) by molecular docking, isothermal titration calorimetry, and photoaffi

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

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

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

119 ectly to Exo70 and is sufficient for exocyst docking, membrane-protein delivery and cell survival.

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

121 erimental results were compared to molecular docking method.

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

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

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

125 enine-based inhibitors using biochemical and docking methods.

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

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

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

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 Whereas the term only improves docking modestly in retrospective ligand enrichment, it

132 A combination of ligand docking, molecular dynamics simulations, and mutagenesis

133 Protein pulldown, molecular docking, molecular dynamics simulations, and patch-clamp

134 ts C-terminal domain and the flanking kinase-docking motif to bind specific HEAT repeats in Rad3.

135 g interactions instead of a single canonical docking motif.

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

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

138 Here, molecular docking of 0.3 million fragments to a crystal structure

139 Molecular docking of AhAI revealed tighter interactions with activ

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

141 -Rab3a into GDP-Rab3a and thus impairing the docking of BDNF vesicles on plasma membranes of astrocyt

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

143 ical crystal growth mechanism comprising (i) docking of clusters from the supersaturated solution ont

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

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

146 Docking of exemplar antagonists from two chemical series

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

148 aling is dependent on recruitment of Syk via docking of its dual SH2 domains to phosphorylated tyrosi

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

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

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

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

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

154 Modeling of docking of oxidizing species on the ds-oligonucleotide w

155 We present an approach for the efficient docking of peptide motifs to their free receptor structu

156 Based on docking of polyols to homology models of transporters, w

157 C2B domain, which may promote the priming or docking of synaptic vesicles.

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

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

160 The docking of the farnesyl group to the hydrophobic pockets

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

162 However, docking of the neck linker to the leading head constrain

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

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

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

166 ty of the cytoplasm in neighboring cells via docking of two connexons expressed in each of the adjace

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

168 nine cluster on the Sgf11 zinc finger domain docking on the conserved H2A/H2B acidic patch.

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

170 ulate protein isotope exchange patterns from docking outputs is described and its utility to guide th

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

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

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

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

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

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

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

178 Our docking predictions correlated well with the cis-favored

179 erved a considerable increase in our protein docking predictions.

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

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

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

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

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

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

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

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

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

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

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

191 oltammetric, photoluminescence and molecular docking responses.

192 A molecular docking result agrees with the model representing rapid

193 ng of 68,752 natural compounds via molecular docking resulted into identification of guanosine 5'-dip

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

195 and are in general agreement with molecular docking results.

196 AND2 physical interaction, and the in silico docking revealed that the same amino acids involved in t

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

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

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

200 Docking screening was performed through identified poten

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

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

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

204 Molecular docking simulations and DNA footprinting experiments sug

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

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

207 Competition assays and molecular docking simulations suggested that HTB1M binds to SOD1 v

208 Molecular docking simulations were conducted for a complete tripep

209 Docking simulations were used to devise a working hypoth

210 uorescence spectroscopy, in silico molecular docking simulations, and in vivo fly and mouse HD models

211 Additional structural features, docking simulations, and mutational experiments characte

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

213 a diprolyl chemical series was modeled using docking simulations.

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

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

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

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

218 ynaptotagmin-1 complex at a synaptic vesicle docking site has to be unlocked for triggered fusion to

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

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

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

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

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

224 gment of hRpn2 that serves as its proteasome docking site; a proline-rich C-terminal hRpn2 extension

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

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

227 1, NPP-4, and NPP-11 primed at multiple Polo-docking sites by Cdk1 and PLK-1 itself physically intera

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

229 poly-SUMOylations of target proteins provide docking sites for distinct adapter and effector proteins

230 g cytokine receptors acting as scaffolds and docking sites for required downstream JAK/STAT proteins.

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

232 lacks specificity for substrates with cyclin-docking sites.

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

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

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

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

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

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

239 Docking studies at hAR structures were performed to rati

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

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

242 Docking studies have explained differential activities o

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

244 In silico molecular docking studies predict that citrate will bind not only

245 Docking studies rationalized the results obtained in the

246 Molecular docking studies revealed a mechanistic model for the int

247 Docking studies revealed binding to the basic surface po

248 Crystallographic and docking studies revealed the main interactions of these

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

250 Docking studies suggest that UBP684 binds to the GluN1 a

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

252 We performed docking studies to understand the interactions of compou

253 Docking studies using available crystal structures have

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

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

256 Docking studies were performed with the synthesized comp

257 Docking studies were performed, and receptor mutants wer

258 hit compounds was undertaken as informed by docking studies, granting a lead compound with a submicr

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

260 s asymmetry, which is supported by molecular docking studies, results from adaptive amino acid change

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

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

263 ar orientations as demonstrated by molecular docking studies.

264 he GPVI receptor have been explained through docking studies.

265 vity analysis, in combination with molecular docking studies.

266 A docking study of the benzoxepin ligands was undertaken.

267 A docking study revealed some critical sites for ATP bindi

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

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

270 Protein docking supported by evolutionary restraints and machine

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

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

273 Docking the model of the FlgK junction onto the structur

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

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

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

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

278 In combination with docking to closed and open state models of TRPA1, photoa

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

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

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

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

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

284 Docking tools are largely used for virtual screening of

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

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

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

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

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

290 from NMR and crystallographic data of domain docking upon ATP binding and undocking in response to AD

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

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

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

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

295 mputational tools such as dihedral scans and docking were used to support this process.

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

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

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

299 Docking with each energy parameter set results in ten mo

300 Docking with these structures can explain several minor