LitCovid-sentences  

PMC:7247521 / 28996-35288 JSONTXT 10 Projects

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Id Subject Object Predicate Lexical cue
T215 0-22 Sentence denotes 3.6 Molecular docking
T216 23-548 Sentence denotes The application of COVID-19 docking server and Discovery Studio software elucidated the interactions between the 20 lead-likeness compounds (S1, W5, MX17, MX16, W11, M5, XO1, MXO1, SO1, WO1, X4, MX8, M3, S5, SX1, O1, X2, X1, O2, MS1) and the 10 nonstructural and 2 structural proteins (Mpro, PLpro, nsp12 [RdRp with RNA], nsp12 [RdRp without RNA], nsp13 [Helicase ADP site], nsp13 [Helicase NCB site], nsp14 [ExoN], nsp14 [N7-MTase], nsp15 [endoribonuclease], nsp16 [2′-O-MTase], N protein NCB site, E protein [ion channel]).
T217 549-603 Sentence denotes The docking scores were depicted in Table 3, Table 4 .
T218 604-748 Sentence denotes The smaller of docking score, the lower of energy would be required, which means the binding between the compounds and the targets are stronger.
T219 749-826 Sentence denotes There are 9 compounds presenting better bonding ability than other compounds.
T220 827-909 Sentence denotes Table 3 Docking score between specific ingredients of QFPD and 2019-nCov proteins.
T221 910-952 Sentence denotes Molecule M3 M5 S1 S5 W11 W5 X1 X2 X4 O1 O2
T222 953-1021 Sentence denotes Main Protease −7.7 −7.3 −6.8 −6.9 −7.2 −7.5 −7.1 −7.9 −7.3 −7.1 −7.4
T223 1022-1093 Sentence denotes Papain-like protease −8.7 −8.5 −9.9 −7.7 −8 −8 −8.4 −8.7 −8.2 −8.6 −8.2
T224 1094-1162 Sentence denotes RdRp with RNA −8.4 −8.5 −8.5 −8.3 −9.1 −9.1 −8.4 −8.2 −8.2 −8.3 −8.6
T225 1163-1234 Sentence denotes RdRp without RNA −6.8 −6.8 −6.9 −6.8 −6.7 −6.9 −7.1 −7.2 −6.5 −7.3 −7.1
T226 1235-1303 Sentence denotes Helicase ADP site −6.3 −6.3 −7.3 −6.5 −6 −6 −6.3 −6.5 −6.2 −6.1 −6.5
T227 1304-1376 Sentence denotes Helicase NCB site −7.9 −6.9 −7.2 −7.1 −7.2 −7.2 −7.4 −7.5 −7.3 −7.4 −7.4
T228 1377-1443 Sentence denotes Nsp14(ExoN) −6.8 −6.6 −6.3 −6.4 −6.9 −6.8 −6.7 −6.9 −6.4 −6.6 −6.9
T229 1444-1512 Sentence denotes Nsp14(N7-MTase) −8.8 −8.1 −8.5 −7.5 −8.4 −8.4 −8.3 −8.5 −8 −8.3 −8.5
T230 1513-1591 Sentence denotes Nsp15(endoribonuclease) −6.6 −6.3 −6.3 −5.9 −6.2 −6.2 −6.2 −6.3 −6.2 −6.4 −6.4
T231 1592-1664 Sentence denotes Nsp16(2′-O-MTase) −7.5 −7.4 −7.5 −7.2 −8.2 −8.2 −7.7 −7.9 −7.7 −7.9 −8.4
T232 1665-1734 Sentence denotes N protein NCB site −7.6 −7.5 −7.8 −7.6 −7.6 −7.6 −8 −8 −7.5 −7.6 −7.6
T233 1735-1810 Sentence denotes E protein(ion channel) −8.1 −7 −7.8 −6.7 −6.4 −6.4 −7.2 −7.3 −7.2 −7.1 −6.8
T234 1811-1839 Sentence denotes M: MXSG, S: SGMH, X: XCH, O:
T235 1840-1847 Sentence denotes Others.
T236 1848-1939 Sentence denotes Table 4 Evaluation of the effect of QFPD on the robustness disturbance of COVID-19 network.
T237 1940-1983 Sentence denotes Topology MXSG SGMH XCH WLS Others BXTM YDBF
T238 1984-2029 Sentence denotes DTS 25.66 26.71 21.02 17.64 23.16 14.52 22.71
T239 2030-2074 Sentence denotes AC −4.63 −5.21 −3.02 −3.49 −5.38 −2.32 −3.78
T240 2075-2117 Sentence denotes APL 13.35 13.40 9.96 6.49 10.66 4.59 11.17
T241 2118-2163 Sentence denotes CoC −1.44 −1.64 −1.59 −1.30 −1.23 −1.15 −1.25
T242 2164-2209 Sentence denotes ClC −6.24 −6.46 −6.45 −6.36 −5.88 −6.46 −6.52
T243 2210-2395 Sentence denotes Average connectivity (AC), Connection centrality (CoC), Closeness centrality (ClC): the larger the quotient is, the more stable the network and, the less the influence made by the drug.
T244 2396-2571 Sentence denotes Disturbance total score (DTS), Average length of shortest path (APL), : the larger the quotient is, the less stable the network and, the larger the influence made by the drug.
T245 2572-2603 Sentence denotes Negative control formula: BXTM.
T246 2604-2635 Sentence denotes Positive control formula: YDBF.
T247 2636-3051 Sentence denotes M3 (Fig. 8A), a specific compound in formulae MXSG, showed eight interactions with E protein [ion channel] including Pi-sigma, Pi-alkyl and Alkyl, which were connected with TYR 57, ALA 32, ILE 46 and PRO 54, etc.; additionally, M3 (Fig. 8B) showed five interactions with nsp13 [Helicase NCB site] including Unfavorable Donor-Donor, Pi-alkyl and Alkyl, which were connected with ASN 559, ARG 409, LEU 42 and PRO 406.
T248 3052-3500 Sentence denotes S1 (Fig. 8C), a specific compound in formulae SGMH, showed seven interactions with nsp13 [Helicase ADP site] including H-bond interactions, van der waals, Amide-Pi stacked and Pi-alkyl, which were connected with ALA 313, ASP 374, GLN 537 and SER 289, etc.; additionally, S1 (Fig. 8D) showed five interactions with PLpro including Pi-anion, Pi-Pi stacked, Pi-Pi T-shaped and Pi-alkyl, which were connected with TYR 264, ASP 164, TYR 268 and PRO 248.
T249 3501-3725 Sentence denotes X2 (Fig. 8E), a specific compound in formulae XCH, showed seven interactions with Mpro including H-bond interactions, Pi-Donor hydrogen bond and Pi-alkyl, which were connected with MET 165, GLU 166, LEU 141 and CYS 145, etc.
T250 3726-3971 Sentence denotes O2 (Fig. 8F), a specific compound in formulae Others, showed seven interactions with Mpro including H-bond interactions, Carbon hydrogen bond, Pi-anion, Pi-sulfur and Pi-alkyl, which were connected with MET 131, GLY 71, LEU 100 and CYS 115, etc.
T251 3972-4425 Sentence denotes MS1 (Fig. 9 A), a compound in formulae MXSG and SGMH, showed eleven interactions with N protein NCB site including H-bond interactions, Pi-Donor hydrogen bond, Pi-sigma, Pi-Pi stacked and Pi-alkyl, which were connected with SER 51, THR 109, ALA 50 and PRO 42, etc.; additionally, MS1 (Fig. 9B) showed five interactions with nsp14 [ExoN] including H-bond interactions and Pi-Pi stacked, which were connected with GLU 92, PHE 190, ASP 273 and VAL 91, etc.
T252 4426-4655 Sentence denotes MX16 (Fig. 9C), a compound in formulae MXSG and XCH, showed seven interactions with nsp15 [endoribonuclease] including H-bond interactions, Alkyl and Pi-alkyl, which were connected with PRO 343, VAL 275, LYS 344 and SER 293, etc.
T253 4656-5025 Sentence denotes SX1 (Fig. 9D), a compound in formulae SGMH and XCH, showed two interactions with nsp14 [N7-MTase] including Pi-Pi stacked and Pi-alkyl, which were connected with PHE 426; additionally, SX1 (Fig. 9E) showed five interactions with nsp15 [endoribonuclease] including H-bond interactions, Alkyl and Pi-alkyl, which were connected with LYS 344, LYS 289, VAL 291 and PRO 343.
T254 5026-5546 Sentence denotes WO1 (Fig. 9F), a compound in formulae WLS and Others, showed seven interactions with nsp16 [2′-O-MTase] including H-bond interactions, Carbon hydrogen bond, Pi-Pi T-shaped, Pi-alkyl and Pi-anion, which were connected with PHE 149, CYS 115, ASP 99 and SER 74, etc.; additionally, WO1 (Fig. 9G) showed seven interactions with nsp12 [RdRp without RNA] including H-bond interactions, Carbon hydrogen bond, Unfavorable Donor-Donor, Pi-cation and Pi-anion, which were connected with THR 556, ARG 553, ASP 623 and SER 682, etc.
T255 5547-5805 Sentence denotes XO1 (Fig. 9H), a compound in formulae XCH and Others, showed ten interactions with nsp12 [RdRp with RNA] including H-bond interactions, Pi-Donor hydrogen bond, Pi-Pi T-shaped and Pi-alkyl, which were connected with CYS 813, GLY 590, LYS 593 and ASP 865, etc.
T256 5806-5935 Sentence denotes Fig. 9 Schematic (3D and 2D) representation that molecular model of common compounds of the five formulae with COVID-19 proteins.
T257 5936-6197 Sentence denotes A: MS1 and N protein NCB site, B: MS1 and nsp14 [ExoN], C: MX16 and nsp15 [endoribonuclease], D: SX1 and nsp14 [N7-MTase], E: SX1 and nsp15 [endoribonuclease], F: WO1 and nsp16 [2′-O-MTase], G: WO1 and nsp12 [RdRp without RNA], H: XO1 and nsp12 [RdRp with RNA].
T258 6198-6292 Sentence denotes MS: MXSG and SGMH, MX: MXSG and XCH, SX: SGMH and XCH, WO: WLS and Others, XO: XCH and Others.