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1 idues 184A, 185, 221A, and 224 (chymotrypsin numbering).
2 esidues 148, 348, 404, and 504 (ovine PGHS-1 numbering).
3 is located at position 290 (Escherichia coli numbering).
4 ), 226(M1), and 254(M2) (using alpha subunit numbering).
5 e Ile16-Asp194 salt bridge (chymotrypsinogen numbering).
6 n the loop at position 159 (Escherichia coli numbering).
7 pped by MCPF-CoA as Cys-114 (mature sequence numbering).
8 , 699, 703, and 710 (chicken skeletal myosin numbering).
9 thylation of residue G2470 (Escherichia coli numbering).
10 ally conserved "perturbing" Lys-194 (E. coli numbering).
11 S(1) pocket (position 189, chymotrypsinogen numbering).
12 ine of the TrkA domain (Y785 in TrkA residue numbering).
13 288L/F290V (all mutants given T. californica numbering).
14 3 and by the residue at position 119 (CYP4A3 numbering).
15 enosine-1518 and -1519 (all Escherichia coli numbering).
16 he residue at position 192 (chymotrypsinogen numbering).
17 putative catalytic Glu-458 (Escherichia coli numbering).
18 been deleted (TolR(62-133), Escherichia coli numbering).
19 on the 39-loop of the protease (chymotrypsin numbering).
20 igosaccharide side chain at position 146 (N2 numbering).
21 s at positions 27, 31, and 34 (based on ChTX numbering).
22 mutated in silico to PVVV (P407V in the 2A79 numbering).
23 residues 81 to 83 and 117 to 122 of HA1 (H5 numbering).
24 with conserved Arg122 (PfDHFR-TS amino acid numbering).
25 d residue for ATP contact is Lys(6)(9) (P2X2 numbering).
26 (superscripts refer to Ballesteros-Weinstein numbering).
27 vative substitutions (N291G and P294K; human numbering).
28 contributions at positions 37 and 69 (pcDHFR numbering).
29 the non-hydrogen-bonded Val 38 (eubacterial numbering).
30 F(2495), NPLY(2519), and DPF(2534) (315-HARE numbering).
31 serine protease domain (G216 in chymotrypsin numbering).
32 STVs are associated with anomalous vertebral numbering.
33 om a population of citizens aged >/=50 years numbering 1.71 million in 2000 and 1.87 million in 2010
35 from four subjects showed additional phyla (numbering 2), genera (numbering 28), and SLOTUs (numberi
37 rRNA nucleotides 2618-2620 (Escherichia coli numbering 2583-2585) and 2541(2506), thereby reorienting
40 of G protein-coupled receptors, the Tas2rs, numbering 3 to approximately 66, depending on the specie
45 terotrimer crystal structure, Glu153 (B'beta numbering) abuts the catalytic site on the C subunit, an
46 A single-site mutation of Pro(101) in EPSPS (numbering according to the enzyme from Escherichia coli)
47 ly identical, with the exception of Met-118 (numbering according to the mature BR sequence), which is
48 hose at positions 36 and 75 modulate fusion (numbering according to the Newcastle disease virus [NDV]
49 stal structures have suggested that Lys-110 (numbering according to the Sulfolobus solfataricus enzym
50 141 and Glu275 are in adenylosuccinate lyase numbering), acts as the general base in most fumarase cl
51 work reaches from betaL328 (Escherichia coli numbering) and betaQ441 via alphaQ399, betaR398, and alp
53 r (15)-NH2 (1) (a somatostatin agonist, SRIF numbering) and H-Cpa (2)-c[DCys (3)-Tyr (7)-DTrp (8)-Lys
54 otein surface (D132, Rhodobacter sphaeroides numbering) and leads to another acidic residue near the
55 superscripts refer to Ballesteros-Weinstein numbering) and non-polar interactions with residues in H
56 modified at the DPhe(7) position (alpha-MSH numbering) and pharmacologically characterized for agoni
57 n modified at the Trp(9) position (alpha-MSH numbering) and pharmacologically characterized for agoni
58 n modified at the His(6) position (alpha-MSH numbering) and pharmacologically characterized for agoni
59 ified the electrophilic cysteine as C759 (B1 numbering) and prepared a mixed disulfide between E. col
60 of both the Weinreb amide at C3 (beta-lactam numbering) and the amino acid side chain at C4 are well-
61 in KD1 interacts with Asp-189 (chymotrypsin numbering) and with the carbonyl oxygens of Gly-219 and
62 ct cells started at amino acid 4 (cystatin C numbering), and displayed reversible inhibition of papai
64 an intestine harbors a beneficial microbiota numbering approximately 10(12) organisms per gram of col
65 O-Alu is a representative of an Alu subclass numbering approximately 400,000 copies, suggesting many
66 , Asp114 (TM3), and Asp118 (TM3) (mouse MC4R numbering) are important for melanocortin-based peptide
67 amembrane residues, Lys-28 and Ser-26 (Abeta numbering), as the critical determinants for efficient i
68 )-Lys(9)-Thr(10)-Cys(11)]Thr(12)-NH(2) (SRIF numbering), at the five known human somatostatin recepto
70 erved serine residues, Ser(18) and Ser(20), (numbering based on isoform 1c) form at least one phospho
71 ked a threonine or arginine at position 319 (numbering based on the HXB2 genome) with AOP-RANTES resi
72 assignment of provisional subtypes, subtype numbering beyond "w," and the nomenclature of intergenot
73 drug-resistance (e.g., H275Y NA mutation [N1 numbering]) but revealed mutations outside the NA active
75 itions 163, 288, 289, 444, and 454 (PsAMADHs numbering) can, directly or not, significantly modulate
76 amino acid position 275 (H274Y, universal N2 numbering), conferring resistance against oseltamivir (T
77 esence of a tyrosine at position 249 (PpNRH1 numbering) confers high hydrolase activity for purine ri
78 There is currently no universally accepted numbering convention for the antiviral drug-related resi
80 ifications, an automated tool for HA subtype numbering conversion, linkouts to disease event data and
82 11 and alanine at positions 35 and 39 (hCRF numbering) decreases CRF1R activity and increases CRF2R
83 2, U2506, U2584, and A2602 (Escherichia coli numbering), demonstrating its potential for the analysis
84 utations at A2451, U2585, and C2063 (E. coli numbering) did not significantly affect either of the re
85 f the two conserved Met252 and Met428 (Kabat numbering) disrupted the interface interactions between
87 ues Asp-179(4.60) and Asp-275(6.58) (residue numbering follows the Ballesteros-Weinstein scheme), wit
88 APP that is phosphorylated at Thr668 (pAPP; numbering for APP695), we show that a phosphorylated, ca
94 served Asn(633) of the PSI PsaB polypeptide (numbering from the Synechococcus elongatus crystal struc
95 ivation region (viz, A or C at position 1002 numbering from the translation start site of Ik-1) withi
96 residues 238-277 (58-97 in chymotrypsinogen numbering) from the protease domain of factor X bound on
98 nd slave oscillators, with groups of candles numbering greater than two, creating a synchronised moti
99 ssociated with drug resistance, NA-R292K (N2 numbering), has been found in some H7N9 clinical isolate
100 involving Glu235 (Glu70 in chymotrypsinogen numbering; hereafter, the numbers in brackets refer to t
101 R157K in the gene encoding hemagglutinin (H3 numbering), I109T in the gene encoding nucleoprotein, an
102 catalytic site (R152W, A246T, and D293N, N2 numbering), (ii) subtype-independent substitutions (E119
103 regions (FIV numbering, with equivalent HIV numbering in superscript): I37(32)V in the active core r
104 nts in common eiders (Somateria mollissima), numbering in the hundreds to thousands of dead birds, ha
105 he7-d-Trp8-Lys9-Thr10-Phe11], L-363,301 (the numbering in the sequence refers to the position of the
108 rotein VP-1 region (positions 1740-1833, Dun numbering) in 49 biopsies obtained from 24 patients with
110 for one residue at the 101st position (Kabat numbering) in CDR3 of the variable heavy chain (V(H)), h
111 ue 399 in the B loop of HA2 (residue 72, HA2 numbering) in different monomers of the trimeric A(H1N1)
112 Arg-15 (bovine pancreatic trypsin inhibitor numbering) in KD1 interacts with Asp-189 (chymotrypsin n
114 Site-directed mutation of Lys-1374 (human numbering) in RBF to Arg or Ile residues almost complete
115 16S rRNA at residues 1540 and 1541 (E. coli numbering) in the anti-Shine-Dalgarno mRNA binding seque
116 Arg(74), Arg(75), and Lys(78) (chymotrypsin numbering) in the catalytic function of activated protei
117 eration of a free radical at Tyr-385 (PGHS-1 numbering) in the cyclooxygenase active site; the Tyr-38
118 ition 292 (using the convention of rhodopsin numbering) in the dolphin LWS cone pigment results in a
119 acing the gatekeeper residue (Thr-338; c-Src numbering) in the inhibitor-binding site with a bulkier
120 on, lysine to glutamine, at position 166 (H3 numbering) in the major antigenic site of HA was reporte
121 ed a cysteine residue at position 442 (EU/OU numbering) in the third constant domain (C(H)3) of the h
122 o acid substitutions at PrP codon 164 (mouse numbering), in the beta2-alpha2 loop region of the prion
123 ifically at amino-acid residue T668 (APP-695 numbering) increases during staurosporine-induced apopto
126 e polymorphisms at -1082, -819, and -592 bp (numbering is relative to the transcription start site).
127 e c oxidase, Asp407 (Rhodobacter sphaeroides numbering) is at the interface of subunit I and subunit
130 ) (superscripts denote Ballesteros-Weinstein numbering) is experimentally observed and appears to be
131 (nucleotides 2042 to 2628; Escherichia coli numbering) is implicated in peptidyltransferase activity
132 1081 of large subunit rRNA (Escherichia coli numbering) is part of a domain targeted by antibiotics a
133 the conserved Trp256 (murine ferrochelatase numbering) is partially responsible for the observed por
134 erved AKR catalytic tetrad, His(120) (AKR1D1 numbering), is substituted by a glutamate in AKR1D1.
135 A2451 in 23S ribosomal RNA (Escherichia coli numbering) led to the proposal of a mechanism of rRNA ca
136 residues 263-271 (using the DENV serotype 3 numbering) located between the two globular domains of N
137 MCADH, while that in LCADH is Glu255 (MCADH numbering), located over 100 residues away in its primar
138 Our calculations show that adding CP-AMPARs numbering <5% of existing synaptic AMPARs is sufficient
139 proteases (residues 143-154 in chymotrypsin numbering) may be responsible for their differential rea
142 additional heteroatom at position 4 (oxazole numbering, N > O > CH) substantially increases activity
143 a carboxylic acid, most likely E-242 (bovine numbering), occurred in P(M) and relaxed back in F.
144 (8)-Lys(9)-Thr(10)-Phe(11)-Cys(14)]-OH (SRIF numbering) (ODT-8) by one of the four conformationally b
145 (8)-Lys(9)-Thr(10)-Phe(11)-Cys(14)]-OH (SRIF numbering) (ODT-8) that is potent at all SRIF receptor s
147 rvey the entire spine and provide definitive numbering of disks and vertebrae was compared with neuro
148 specially the Arg238-Glu459 salt bridge (the numbering of residues follows myosin II in Dictyostelium
149 ote: In the AOP version of this article, the numbering of the author affiliations was incorrect.
151 ided with the original annotations and plate numbering of the paper atlas and enable viewing the mate
152 nd Arg134 constitute the catalytic site; the numbering of the residues includes the signal sequence.
153 ality was evaluated by using visual scoring, numbering of visible bronchi, and quantitative measureme
154 amino acids 326-336 (143-154 in chymotrypsin numbering) of factor X (fX) comprise a flexible surface
155 ent study indicated that Tyr99 (chymotrypsin numbering) of factor Xa and Thr99 of activated protein C
157 loops (amino acids 143-154, chymotrypsinogen numbering) of plasma serine proteases play key roles in
160 mediated by the residue at position 374 (HA0 numbering) of the HA2 subdomain as critical for HA trime
161 structured portion (residues 7-29, glucagon numbering) of the micelle-bound 27-residue peptide is 1.
162 acids [aa] 61 to 87 using PB1-F2 amino acid numbering) of the PB1-F2-derived C-terminal peptides fro
163 le mutant (F86L/T93P/S118T; bovine rhodopsin numbering) of the tiger salamander UV cone pigment appea
165 -Phe-Trp(8)-Lys-Thr-Phe-Cys-OH (somatostatin numbering; OLT-8, 9) substituted by imBzl-l- or -d-His a
166 When attacking an Utetheisa egg cluster (numbering on average 20 eggs), the larva subjects it to
167 ve site of 23S rRNA, A2602 (Escherichia coli numbering), on the peptidyl transferase activity of the
168 ential RNA (RPR) and protein subunits (RPPs) numbering one in bacteria, and at least four in archaea
169 -I222T, rg-H274Y, rg-N294S, and rg-R371K, N2 numbering) or zanamivir (rg-E119A and rg-R371K) failed t
170 s loop (residues 143-154 in chymotrypsinogen numbering) plays a pivotal role in determining the macro
171 ates that amino acid residue 90 (B. fragilis numbering) plays an important role in conferring substra
172 n of APP, lysine 624, on the basis of APP695 numbering (position 28 relative to Abeta) that plays a c
173 An arginine (R481) (Rhodobacter sphaeroides numbering), positioned between the D-propionates of the
174 ution occurred at C(10) and C(9a) (mitomycin numbering) providing a CD(3) ether and a CD(3) hemiamina
175 4R, C725S, A728S, D730S, and C731S (Na(v)1.4 numbering) reduced block of Na(v)1.4 by 4-, 86-, 12-, 18
176 s3-Xxx7-DTrp8-Lys9-Thr10-Cys14]-Thr-NH2 (the numbering refers to the position in native SRIF), with X
177 y(8)-Lys(9)-Thr(10)-Zzz(11)-Cys(14)]-OH (the numbering refers to the position in native SRIF), with X
179 he other extends from positions -73 to -103 (numbering relative to the transcription start site of cf
180 ted at sites 1917 and 1951 (Escherichia coli numbering), respectively, in the 23S rRNA gene of C. bur
181 rt, and integrase), in which the amino acid numbering restarts at the first codon position of each d
182 yrosyl radical on R2 (Y122, Escherichia coli numbering) reversibly generates the transient thiyl radi
184 utein sequence begins with Gly121 (using the numbering scheme for the wild-type protein) and terminat
185 a conserved cysteine residue at position 83 (numbering scheme of the 140-residue form of FGF-1).
186 2 (TM7) equivalent to Lys(7.45) (Ballesteros numbering scheme) involved in covalently attaching retin
189 nnotate sequences with the five most popular numbering schemes: Kabat, Chothia, Enhanced Chothia, IMG
190 ressed by phosphorylation at Ser287 (Xenopus numbering; Ser216 of human Cdc25C) and subsequent bindin
192 saturated acyl chains at the stereospecific numbering (sn)-1 position from PC and likely a channelin
193 st that plant CPS prefers the stereospecific numbering (sn)-1 position whereas E. coli CPS acts on sn
195 d to Cys-305 (Cys-331 in human type II IMPDH numbering), suggesting that Cys-305 functions as a nucle
196 achieved by the use of a computer encrypted numbering system at the National Cancer Institute) and b
199 (residue -34 to -15 and -11 to +6, using the numbering system in which the conserved histidine residu
202 otrypsin numbering system; for the urokinase numbering system it is Ile(159)-Lys(404)) and two point
205 at position +4 in the beta-polypeptide (the numbering system used assigns position 0 to the His whic
206 in lacking the N-terminal pyroglutamate (the numbering system used has Asp2 as the N-terminal residue
208 m label was located at positions (patchoulol numbering system) C5 (both isotopomers, ca. 100%) and C1
209 rg59+Asn108 mutants (using the P. falciparum numbering system) exhibit no significant fitness defects
210 H310A, H435Q, H435R, and H310A/H435Q, Kabat numbering system) expressed well in mammalian cell cultu
212 group of His157 (His159 in the yeast enolase numbering system) is in van der Waals contact (4.5 A) wi
213 acidic residue at position 144 (chymotrypsin numbering system) is the primary determinant of the dist
216 riants (I253A, H310A, and H310A/H435Q; Kabat numbering system) that exhibited differential serum pers
217 Lys65, His66, and Tyr71 (using the thrombin numbering system), that were resistant to HCII inhibitio
218 due that occupies position 192 (chymotrypsin numbering system), which plays a pivotal role in determi
219 man, were aligned, using the now-known Kabat numbering system, and a quantitative measure, variabilit
220 equences were also aligned using a different numbering system, since the locations of their CDRs (31-
223 sidues Ile(16)-Lys(243) (in the chymotrypsin numbering system; for the urokinase numbering system it
226 erases of the exocyclic N6 of A2058 (E. coli numbering) that forms the macrolide binding site in the
227 e insertion loop at residue 60 (chymotrypsin numbering) that has been implicated in modeling studies
228 rm of the Abl tyrosine kinase (H396P; Abl-1a numbering) that is resistant to the Abl inhibitor imatin
229 fide bond (Cys(191)-Cys(220) in chymotrypsin numbering) that links two beta-loop structures that defi
230 g-73, Arg-75, and Arg-77 in chymotrypsinogen numbering) that play key roles in the function of thromb
231 ines, R481 and R482 (Rhodobacter sphaeroides numbering), that interact directly with heme a and the h
232 D132(I) (subunit I; Rhodobacter sphaeroides numbering), the entrance of the K-channel has not been c
233 1) at Thr(697) and/or Thr(855) (rat sequence numbering) to inhibit phosphatase activity and increase
234 dine residue (His-287, murine ferrochelatase numbering) to leucine and reduced over 2 orders of magni
235 and that the NPXY tyrosine (Tyr743 by APP751 numbering, Tyr682 in APP695) is required for APP endocyt
236 hour) could be obtained via parallelization (numbering up) by simply wrapping several membrane tubing
237 ing of the base at position 1492 (by E. coli numbering) upon binding to the E. coli rRNA A site, but
239 ted that aspartate 143 (Escherichia coli TGT numbering) was involved in heterocyclic substrate recogn
240 eophilicity at the delta10 double bond (GGPP numbering) was synthesized and incubated with taxadiene
241 nizes MYPT1 phosphorylated at Thr(654) (M130 numbering), we determined that this calcium-independent
243 esidues (Tyr(677) and Tyr(701), using hFGFR1 numbering) were essential for bioactivity, but the remai
244 Arg73, Arg75, and Arg77 in chymotrypsinogen numbering) were individually substituted with a Glu.
245 F linkage sites (using the original sequence numbering) were residue 39, which is at the beginning of
246 s(230), Arg(233), and Lys(239) (chymotrypsin numbering) were substituted with Ala in separate constru
247 teine at positions 3 and/or 14 (somatostatin numbering) were/was substituted with d-cysteine, norcyst
248 e chains of two residues, S353 and T354 (NIS numbering), were identified as the Na(+) ligands at Na2.
249 tion, two substitutions, H274Y and R292K (N2 numbering), were introduced into each NA gene for compar
250 , or dual sulfation at both positions (Kabat numbering where H designates heavy chain) leads to an in
251 s Ser236 (Dictyostelium discoideum myosin II numbering) which was proposed to be involved in a hydrog
252 ucleotide at position 1408 (Escherichia coli numbering), which is an adenosine in prokaryotic ribosom
253 This preference is linked to Phe902 (human numbering), which is responsible for low-affinity bindin
254 d, with the single exception of Glu-22 (IL-3 numbering), which is strictly conserved but nonetheless
255 ntains an aspartate residue [Asp157 (spinach numbering)], which is highly conserved in eukaryotic and
256 on, VRVIII (amino acids 586 to 591 [AAV8 VP1 numbering]), which lies on the surface of the protrusion
257 Arg-173, Lys-175, and Lys-179; chymotrypsin numbering) with Ala, using an expression system that all
258 0d, K60f, E217, and R221 in chymotrypsinogen numbering) with alanine altered the substrate specificit
259 ite Ser-581 (full-length fatty acid synthase numbering) with alanine completely eliminated catalytic
260 His42, His124, and Glu126 (Aquifex aeolicus numbering), with particular attention paid to the effect
261 combinations of three critical regions (FIV numbering, with equivalent HIV numbering in superscript)
262 itions 1345-1350/1372-1376 (Escherichia coli numbering), within the three-way junction loop, which bi
263 rporation of a quaternary center at C-6 (THP numbering) would restore the facial selectivity with mor
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