コーパス検索結果 (1語後でソート)
通し番号をクリックするとPubMedの該当ページを表示します
1 re studied with the QM/MM method ONIOM(B3LYP:AMBER).
2 rock and as inclusions in fossilized resins (amber).
3 n Collembola (the first is also preserved in amber).
4 ototransistors from 495 nm (blue) to 590 nm (amber).
5 f any phytophagous insect group preserved in amber.
6 force fields available for RNA, the parmbsc0 AMBER.
7 iments using a 20-million-year-old Dominican amber.
8 Ma older than the earliest prior records in amber.
9 croscopic "conservation traps" comparable to amber.
10 and three-dimensional specimens preserved in amber.
11 d-Cretaceous (ca. 100 Mya) Myanmar (Burmese) amber.
12 ophoroideans from the mid-Cretaceous Burmese amber.
13 but occasionally they are well-preserved in amber.
14 tra are found only in much younger Dominican amber.
15 with specialized programs such as CHARMM or AMBER.
16 ids from two specimens of fossil feathers in amber.
17 the few mantidflies hitherto described from amber.
18 ine rove beetles from mid-Cretaceous Burmese amber.
19 in Data Bank files via the cpptraj module in AMBER.
20 tudies of protein preservation in fossils in amber.
21 emidid damselfly from mid-Cretaceous Burmese amber.
22 at are exclusively described from Cretaceous ambers.
28 e potentials, including a new variant of the AMBER-99 force field, denoted AMBER-99 phi, which shows
29 variant of the AMBER-99 force field, denoted AMBER-99 phi, which shows improved agreement with experi
30 Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNA(Pyl) mutants were
33 ing evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands
35 ized orthogonal translation system that uses amber and evolved quadruplet-decoding transfer RNAs to e
40 ial molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exc
41 ith comedication, the prevalence of combined amber and yellow PDDIs was 43% (33% amber - mostly with
44 mbion compactus gen. et sp. nov., in Burmese amber ( approximately 99 million years old), displaying
46 (new family)] from Early Cretaceous Burmese amber (approximately 100 million years before the presen
47 eptor (A), and a photo-insensitive molecule (Amber) as a nonfluorescent (N) place holder: namely, NDA
50 ular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squ
55 yl- l-phenylalanine (Bpa) in response to the amber codon allowed the biosynthesis of Bpa-substituted
56 ded this unique amino acid in response to an amber codon allowing a single 1 to be placed at any loca
57 n from approximately 20% to >60% on a single amber codon and from <1% to >20% on two amber codons.
66 the radical trap 3-amino tyrosine (NH2Y) by amber codon suppression at positions Y731 or Y730 and in
69 ite-specific incorporation into proteins via amber codon suppression in Escherichia coli and mammalia
70 vo incorporation of unnatural amino acids by amber codon suppression is limited by release factor-1-m
71 S can be redesigned to achieve high-fidelity amber codon suppression through delivery of p-bromopheny
73 site-specific introduction into proteins via amber codon suppression using the wild-type pyrrolysyl-t
78 g the efficiency of suppression at a gene II amber codon upstream from the gene X start, the already
81 cognate orthogonal tRNA that recognizes the amber codon, are encoded on the plasmid pSUPAR6-L3-3SY,
82 ecodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthog
83 efficiently incorporated at a predefined UAG amber codon, thereby competing with RF1 rather than RF2.
84 system that site-specifically--using the UAG amber codon--inserts Sec depending on the elongation fac
93 be a new specimen of enantiornithine bird in amber, collected at the Angbamo locality in the Hukawng
94 cent experimental observation of the unusual amber coloration of aluminum doped sol-gel glass that ha
95 ter stability i.e. 63 days when stored under amber-colored vial compared to only 35 days when stored
97 superinfection immunity of phages to enrich amber-containing clones, thus avoiding the observed bias
99 an remains trapped in Cretaceous-age Burmese amber continue to be uncovered, revealing a diversity of
102 rrolysine requires the pylT gene product, an amber-decoding tRNA(Pyl) that is aminoacylated with pyrr
103 This discovery highlights the potential of amber deposits to reveal the lowest limits of vertebrate
105 may have contributed to the formation of the amber droplets, but we find that the abundance of amber
106 droplets, but we find that the abundance of amber during the Carnian (ca. 230 Ma) is globally anomal
108 m mass spectrometry revealed the mass of the amber-encoded residue in MtmB, MtbB, and MttB as 237.2 +
109 and feather development of DIP-V-15103, the amber-entombed tail section that we recently reported [2
110 stinct from other Mesozoic assemblages, with amber entrapment including representatives from unusual
113 h a force field, the relative weights of the Amber ff03 all-atom potential supplemented by an explici
114 ll-atom molecular dynamics simulations using AMBER FF03 and the generalized-Born solvation model.
115 d-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation
117 "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structure
118 he relative weights of the components of the Amber ff03 potential on a large set of decoy structures
119 figurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A
121 h an optimized all-atom protein force field (Amber ff03w) and an accurate water model (TIP4P/2005) to
122 an 0.8 mus MD simulation computed using the Amber ff10 force field as well as to determine an atomic
125 s by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR vali
127 g of residue charges for charged residues in Amber ff99SB( *) significantly improves their helix prop
132 d flagged), of potential clinical relevance (amber flagged) or of weak clinical significance (yellow
133 hlights the unique preservation potential of amber for understanding the morphology and evolution of
135 inst various types of experimental data, the AMBER force field ff99SB was benchmarked in recent years
136 h B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine t
137 Molecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over
142 ble, those obtained using last generation of AMBER force-fields (BSC1 and BSC0OL15) show predictive p
143 le isotope composition (H and C) suggest the amber formed from resins exuded by cupressaceous conifer
144 nsistent with previous suggestions that this amber formed on an island within the Trans-Tethyan arc(1
150 nchans found as inclusions in mid-Cretaceous amber from Kachin state (northern Myanmar), which repres
151 ved in mid-Cretaceous ( approximately 99 Ma) amber from Kachin State, Myanmar [17], with plumage stru
153 quisitely preserved myxomycete sporocarps in amber from Myanmar, ca. 100 million years old, one of th
154 preserved in Early Cretaceous (ca. 100 mya) amber from Myanmar, one described as Krishnatermes yoddh
155 tebrate remains trapped in middle Cretaceous amber from northern Myanmar [1, 2] have provided insight
156 lusions in approximately 99-million-year-old amber from northern Myanmar provide unprecedented insigh
159 f a green lacewing larva in Early Cretaceous amber from Spain with specialized cuticular processes fo
161 xylid fossils in mid-Cretaceous and Cenozoic ambers from Myanmar (ca. 99 million years ago [Mya]), Ru
162 files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/Open
163 itive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulat
167 sible traces of colour, while discoveries in amber have been disassociated from their source animals.
168 With the taxa reported herein, the Mexican amber holds the greatest diversity of fossil copepods wo
169 All the honeys, except for a Malaysian "Amber honey" stimulated the release of TNF-alpha from mo
172 roplebeia dominicana, recovered from Miocene amber in the Dominican Republic, that is 15-20 million y
173 esy in 16 million-year-old Miocene Dominican amber involving a springtail being transported by a mayf
177 anine-related phenotypic suppression of lacZ amber is enhanced by mutations in genes related to the p
179 rther recovery of arthropods in Carnian-aged amber is promising and will have profound implications f
180 The preservation of aquatic arthropods in amber is unusual but offers a unique insight into ancien
182 ies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenz
187 of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather prese
188 combined amber and yellow PDDIs was 43% (33% amber - mostly with cardiovascular drugs - and 20% yello
190 with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielde
192 h a mutant N4 isolate (N4am229) harboring an amber mutation in Orf65 yielded virions containing (N4gp
195 ne, was genetically encoded in E. coli by an amber nonsense codon and corresponding orthogonal tRNA/a
196 oded in Saccharomyces cerevisiae by using an amber nonsense codon and corresponding orthogonal tRNA/a
200 amino acids in response to three independent amber nonsense codons in sperm whale myoglobin or green
202 Here we report new Pangean and Gondwana amber occurrences dating from ~230 to 40 Ma from Austral
203 using the beta-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the seri
205 lized pollination mode from Early Cretaceous amber of Spain, wherein four female thrips representing
209 zations, parm99chi_YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between s
210 arger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably po
211 bly robust predictions, while that of PARSE, AMBER parm99, and AMBER ff03 performed more poorly.
212 cations according to packaging material (PET amber, PET transparent and tinplate can) and light expos
214 Here, dark pseudoinclusions in kidney-shaped amber pieces from the Early Cretaceous (Albian) amber fr
215 om simulations under several variants of the AMBER potential in explicit solvent using a global distr
220 materials, such as limestone, claystone, or amber, provide detailed information on extinct species t
221 rich deposits of 99 million-year-old Burmese amber resolves ambiguity regarding sociality and diversi
223 ight characteristics and feathers in Burmese amber reveal how multi-dimensional functionality can be
225 t evidence in 99 million-year-old Cretaceous amber showing that hard ticks and ticks of the extinct n
226 tic affinities to those from coeval European ambers, showing a biotic interchange between the eastern
227 the unique fossilisation environment inside amber shows potential for the recovery of ancient amino
228 persists for at least 1 mus, whereas in the AMBER simulation, it remains highly dynamic; additional
229 The simulations were carried out using the Amber software on inexpensive GPUs, providing approximat
230 A. margulisae from Late Albian Penacerrada I amber (Spain) possess four pairs of rudimentary oostegit
231 ribed from ca. 105-million-year-old San Just amber (Spain), representing the oldest and one of the fe
233 McKellar et al. analyzed Late Cretaceous amber specimens from Canada and identified some filament
234 respond to droplets of phloem sap containing amber spheroids and preserving both organic and inorgani
236 amino acid incorporation in response to the amber stop codon (UAG) in mammalian cells is commonly co
237 n of different amino acids in response to an amber stop codon by utilizing switchable designer transf
246 nical translation machinery and can suppress amber stop codons to incorporate selenocysteine with hig
251 in vitro translation of mRNAs containing an amber-stop codon in the signal peptide in the presence o
252 The calculations were performed using the AMBER suite of programs and the parm94 force field, vali
253 ) calculations were then performed using the AMBER suite to validate the newly generated force field.
254 nce of RF1, however, endogenous near-cognate amber suppressing tRNAs can lead to contaminating protei
260 -coumarin-yl)-ethylglycine, using orthogonal amber suppression machinery in Escherichia coli MS metho
261 st incorporated into phage libraries through amber suppression nearly two decades ago, their applicat
262 in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and ele
266 mino acids (ncAAs) by introducing orthogonal amber suppressor aminoacyl-tRNA synthetase/tRNA pairs in
267 ylation modulates RAD52 function, we used an amber suppressor technology to substitute tyrosine 104 w
268 eRS (T415G) and a mutant yeast phenylalanine amber suppressor tRNA (ytRNAPheCUA_UG) into an E. coli e
269 ystem, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus
271 suppressor tRNAs are less efficient than the amber suppressor tRNA THG73 (Tetrahymena thermophila G73
272 g aminoacyl-tRNA synthetases aminoacylate an amber suppressor tRNA with a desired unnatural amino aci
273 enes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on
274 on levels of the orthogonal Escherichia coli amber suppressor tRNA(CUA) and cognate aminoacyl-tRNA sy
278 don with high efficiency using an orthogonal amber suppressor tRNA/aminoacyl-tRNA synthetase (aaRS) p
279 was responsible for misacylating the initial amber suppressor version of the yeast tryptophanyl tRNA.
281 hogonal pairs, including three highly active amber suppressors, and evolve new amino acid substrate s
283 id residues in Ste2p with Bpa by engineering amber TAG stop codons into STE2 encoded on a plasmid.
284 rolysine, the 22nd amino acid, is encoded by amber (TAG=UAG) codons in certain methanogenic archaea a
285 a 28 bp deletion that introduces a premature amber termination codon into the open reading frame of a
286 gment of a fertile leaf preserved in Burmese amber that represents the first fossil evidence of the f
287 preserved feathers in mid-Cretaceous Burmese amber that share macro-morphological similarities (e.g.,
288 leaves enclosed in a piece of Eocene Baltic amber that share relevant morphological features with ex
290 (Staphylinidae) from mid-Cretaceous Burmese amber, the latter belonging to Oxyporinae, modern member
291 band (NEB) technique has been implemented in AMBER to calculate low-energy paths for conformational c
292 d specimens have been described from Burmese amber: two isolated wings, an isolated foot with wing fr
297 of fossilized remain, abundant in Cretaceous ambers, was first interpreted as fossilized vacuole-bear
298 irst skeletal remains of avians preserved in amber were described in 2016, new avian remains trapped
299 rap-jaw ant from 99 million-year-old Burmese amber with head structures that presumably functioned as
300 Mesozoic and Cenozoic fossilized tree resin (amber) with few findings from the high southern paleolat