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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 uman pathogenic mutations and toxic antibody docking.
8 ing Giardia's cell shape and guiding axoneme docking.
9 hat precisely orient objects-and use them to dock a DNA-binding protein on a double-helix stage that
11 sequence; (ii) an in silico peptide-protein docking analysis and in vitro binding assay that identif
12 ratory conditions was not noticed, in silico docking analysis supports allosteric binding to glutamat
13 ether with binding energies measurements and docking analysis, pointed out pelargonidin 3-robinobiosi
14 e in this process, which they describe as a "dock and lock." This finding not only significantly enha
15 ning the v-SNARE synaptobrevin 2, which were docked and fused with lipid-labeled PSMs containing the
19 osetta software for macromolecular modeling, docking and design is extensively used in laboratories w
20 hyaluronan receptor 1 (LYVE-1) mediates the docking and entry of dendritic cells to lymphatic vessel
30 ith the extracellular loops, predicted using docking and molecular dynamics simulation with newly con
32 orter assays, chromatin immunoprecipitation, docking and molecular dynamics simulations, human unfold
36 analyses of fluorescence spectra, molecular docking and quantum-chemical calculations at DFT level.
38 meric lattice-structured platform for capsid docking and recruit viral and cellular NEC-associated fa
39 and X-ray scattering data with comprehensive docking and refinement revealed how XPA DBD and RPA70AB
40 studies establish a high-resolution channel-docking and resting-state locking mechanism for huwentox
41 Here, the constructed structural models, docking and scoring schemes were validated by their abil
43 tudy demonstrates that refined computational docking and simulation studies combined with experiments
45 ation of state-of-the-art tools in molecular docking and simulations, including an in-house simulatio
47 orthosteric binding site by using molecular docking and structure-based drug design to optimize liga
48 to the MHC-I T-cell epitopes using molecular docking and the complexes were relaxed with molecular dy
51 analysis, bio-kinetics simulation, molecular docking, and dynamics studies were performed for the sel
52 matics-based structure modelling, Cu(2+) ion docking, and MD simulations of peptide-MBP chimeras corr
53 logical profiles, including rate of killing, docking, and molecular dynamics studies, suggest that ou
54 SD17B10 was further evaluated using molecule docking, and results showed that MEHP has higher affinit
56 f the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional intera
57 , synapse and active zone structure, vesicle docking, and transsynaptic nano-organization were unimpa
58 sic Xase complex occurs through a multistep "dock-and-lock" pathway in which the initial interaction
60 tudy, we applied a structure-based molecular-docking approach to find small molecules that specifical
63 assification model) and structure (molecular docking) based for identifying possible sweeteners from
64 Cross-validated using the protein-protein docking benchmark version 5.0, our method (ZING) achieve
70 surements, NMR titrations, and computational docking calculations, as well as biological investigatio
73 in cargo trafficking pathways by sorting and docking cargos for translocon-mediated transport across
75 n the recent rounds of blind protein-protein docking competition CAPRI (Critical Assessment of Predic
77 n of the major components of the peroxisomal docking complex Pex14p/Pex17p, in a native bilayer envir
78 present iScore, a novel approach to scoring docked conformations that combines HADDOCK energy terms
81 rogress, reliably distinguishing near-native docking conformations from a large number of candidate c
82 SO in finding both low-energy and small-RMSD docking conformations with high robustness in most cases
83 ict the general position of the Dimerization/Docking (D/D) domain, which is essential for localizatio
84 l titration nanocalorimetry (ITC), molecular docking (DC), and molecular dynamics (MD) were used to c
85 nal deep neural network-based approach named DOcking decoy selection with Voxel-based deep neural nEt
90 ring a comprehensive annotation of available docking domains information in bacterial biosynthetic pa
91 , and associated the histidine substrate and docking domains with the kinase core, thus preventing ca
92 ical peptide region that engages a substrate docking exosite and a C-terminal transition-state analog
93 cement experiments demonstrate that both the docking exosite and the active site are engaged by the b
94 native structural conformations from protein docking experiments and outperform other contact-based p
95 esults of the steered molecular dynamics and docking experiments indicated that the canonical PLB-bin
96 ecular dynamics and membrane protein-protein docking experiments to achieve both a global search and
97 he saccharide core of PG using computational docking experiments, and multiangle light-scattering exp
98 ther probed and rationalised using molecular docking experiments, which indicated that conjugated hal
102 ecificity, as RAC2(E62K) is activated by the DOCK GEF, DOCK2, but not by the Dbl homology GEF, TIAM1,
104 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D str
105 of Opa1 (l-Opa1) is sufficient for membrane docking, hemifusion and low levels of content release.
106 ed by clusters of Munc13, which allow SVs to dock in defined nanoscale relation to Ca2+ channels.
114 and two YefM dimers with N-terminal domains dock into the adjacent major grooves of DNA to specifica
115 orubicin and verapamil, which were initially docked into the ABC transporter, get translocated throug
116 o position the CXCL12 N terminus for optimal docking into the orthosteric pocket of CXCR4 and suggest
119 design and development, and flexible ligand docking is a widely used method for docking simulations.
120 nd fully replenish the docked pool, but this docking is transient and they either undock or fuse with
123 bound to rodent brain sections or ADAM22/23-docked LGI1, but all inhibited the docking of LGI1 to AD
124 of the largest and freely available ready-to-dock ligand libraries, with more than 1.4 billion commer
125 ions is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, po
126 rstand how menthol activates the channel, we docked menthol to the channel and systematically validat
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
130 r modeling study, based on a receptor-driven docking model and including a systematic free energy per
134 n vitro immuno-infrared sensor measurements, docking, molecular dynamics simulations, and ab initio c
135 we combine spectroscopic data with molecular docking, molecular dynamics, and excitonic quantum/molec
138 rovide a general method for surveying viable docking motif sequences and quantifying their potency in
139 assay to comprehensively characterize the LP docking motif, which determines G1-CDK substrate specifi
140 yeast, CDK substrates with Leu/Pro-rich (LP) docking motifs are recognized by Cln1/2 cyclins in late
141 ng eukaryotic cell division, cyclin-specific docking motifs help cyclin-dependent kinases (CDKs) phos
142 fying enzymes recognize their substrates via docking motifs, but the range of functionally permissibl
143 TP and NSAC1003 are competitive; computation docks NSAC1003 into RecB's ATP-binding site, suggesting
150 p98-Rae1 via its C-terminal domain to impair docking of cargo-receptor (karyopherin/importin) complex
151 Its activity is temporally regulated by the docking of different activating subunits, known in plant
152 ze the biological effect of GK-15, molecular docking of GK-15 into the N-terminal extracellular ligan
153 the epitaxial growth is enhanced by lateral docking of hBN to Cu (111) steps, ensuring the mono-orie
154 mpact structure than that predicted from the docking of homologous crystal structures of the separate
156 ides selective recognition and high-affinity docking of large dense core secretory vesicles to the pl
158 ne cassettes is proposed, based on molecular docking of plant metabolites within the ATP and D-cyclos
159 substrate channels, combined with in silico docking of SAM in holo MtNifB, suggests the binding of S
162 release at the presynaptic terminal requires docking of synaptic vesicles to the active zone membrane
165 Recent models suggest that intramolecular docking of the MIDAS domain onto the AAA ring is require
170 ion to light-dependent activation, "envelope docking" of ACCase permits fine-tuning of fatty acid sup
171 verage stable AT1R was used as a template to dock Olmesartan via AutoDock 4.2, MOE, and AutoDock Vina
173 inclusions, as well as multivesicular bodies docked on the inclusion surface, both of which were immu
174 ction with H2A-H2B, allowing FACT-H2A-H2B to dock onto a complex containing DNA and histones H3 and H
175 scent chain grows, emerging helical segments dock onto each other and continue to rearrange at the vi
176 peller domain of its trimerisation region to dock onto the side of the helicase assembly formed by Cd
178 osed that different S-components compete for docking onto the same ECF module, but a minimal liposome
179 pre-insertion OCCM," the main body of Mcm2-7 docks onto ORC-Cdc6, and the origin DNA is bent and posi
180 rpL5, rpL11, Rpf2 and Rrs1, which initially docks onto the flexible domain V of rRNA at earlier stag
181 of indole on DNA gyrase predicts that indole docks perfectly to the ATP binding site of the GyrB subu
182 sicles are recruited and fully replenish the docked pool, but this docking is transient and they eith
183 the closest ideal Cn symmetric complex from docking poses containing a homo-dimer without prior know
189 hen searches for templates and uses them for docking, presenting the user with top-scoring poses and
190 ness in solving both holo- and apo-structure docking problems with different numbers of torsions, whi
194 the cargo-loaded receptor interacts with the docking protein Pex14p that is tightly associated with P
196 ions, including an in-house simulation-based docking protocol, to investigate the binding properties
199 This in vitro evidence was corroborated by docking results demonstrating favorable interactions bet
201 rther structural analyses with computational docking results uncover the differences between CB2 and
204 anuphilin, is a Rab effector responsible for docking secretory vesicles to the plasma membrane before
210 were strategically redesigned by performing docking simulation, following surface-electrostatic pote
214 oviding strong insights to improve molecular docking simulations, especially regarding the interactio
215 An in silico structural approach based on docking simulations, pharmacophore modeling and molecula
220 ons between the LC3-interacting region (LIR) docking site (LDS) in ATG8s and LIR motifs in various in
221 ex formation with LegK7 but also served as a docking site for downstream substrates such as the trans
222 in 153 (Nup153), which is known to provide a docking site for protein-cargo complexes at the nuclear
223 ation of CD5 tyrosine 429, which serves as a docking site for proteins with adaptor functions (c-Cbl,
224 stone H3 at threonine-3 (H3T3ph), creating a docking site for the Chromosomal Passenger Complex (CPC)
225 ecular-level characterization identified the docking site on PrP(C) that underlies the stereoselectiv
226 sed to pattern RhoA activation by creating a docking site on the central spindle that concentrates th
227 viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively g
228 rsible tPAINT probe that exposes its cryptic docking site permanently and thus integrates force histo
229 engineered reversible probes with a cryptic docking site revealed only when the probe experiences fo
230 ination of homology protein modeling, ligand docking, site-directed mutagenesis, and electrophysiolog
233 of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST deca
234 ic1, contains linear phosphorylation motifs, docking sites, and phosphodegrons to empower an N-to-C t
236 imulations show that the regulatory segments dock spontaneously at the interface between hub subunits
237 reviously, we observed a loosely and tightly docked state preceding leaflet merger using arresting po
240 the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand
241 2.2 and DQ2.2-glut-L1 (PFSEQEQPV) revealed a docking strategy, and associated interatomic contacts, w
242 y in vivo, and they reveal how variations in docking strength can tune the degree and timing of regul
244 zyme, protein mass spectrometry analysis and docking studies allowed us to gain an insight into the i
250 logy model of GPR84 was generated to perform docking studies rationalizing the experimental data.
262 1) in silico, where modeling ligand-protein docking suggested that 6-OH-BDE-47 is a promiscuous ATP-
266 mechanistic insight, combined with simulated docking techniques, allows for the design and optimizati
269 tropomyosin or actin-tropomyosin yet avoided docking TnT domains that lack known or predicted structu
270 tional domains (SAND, PHD, bromodomain) that dock to DNA or post-translationally modified histones an
271 We reveal how mechanoregulatory complexes dock to doublet microtubules with regular 96-nm periodic
274 roximal effects of GLUT4-containing vesicles docking to and fusion with the PM, also directly regulat
276 on-demand" virtual library, we used covalent docking to identify arylsulfonyl fluorides that target a
277 king mass spectrometry (XL-MS) and molecular docking to interrogate the three-dimensional architectur
278 .9 angstrom resolution which allows us using docking to suggest a mechanism of interaction between co
280 This results in erroneous, lateral centriole docking to the nucleus, leading to spermatid decapitatio
285 , we first employed unbiased protein-protein docking tools to identify binding specificity of individ
294 recently, a new predictive method, reactive docking, was developed, building on the growing corpus o
295 l assays, structural modeling, and molecular docking, we demonstrate that Endosidin20 (ES20) targets
298 tional analyses of the benzanilide structure docked with human HDAC8 enzyme showed the adoption of a
299 though some flexibility in how the AAA+ ring docks with ClpP may be necessary for optimal function.
300 timal colonized salt marsh ecosystem, and on docks within the marsh, an artificial mangrove analogue.