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PMC:7755033 / 97366-104009 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1880 1328-1333 Gene denotes spike Gene:43740568
1881 784-789 Gene denotes spike Gene:43740568
1882 120-125 Gene denotes spike Gene:43740568
1883 227-230 Gene denotes PDB Gene:5131
1884 151-154 Gene denotes PDB Gene:5131
1885 109-119 Species denotes SARS-CoV-2 Tax:2697049
1886 194-204 Species denotes SARS-CoV-2 Tax:2697049
1887 773-783 Species denotes SARS-CoV-2 Tax:2697049
1888 1025-1035 Species denotes SARS-CoV-2 Tax:2697049
1889 1319-1327 Species denotes SARS-CoV Tax:694009
1890 1385-1395 Species denotes SARS-CoV-2 Tax:2697049
1891 1411-1414 Gene denotes PDB Gene:5131
1892 1348-1351 Gene denotes PDB Gene:5131
1893 814-825 Chemical denotes withanolide MESH:D054358
1894 1367-1378 Chemical denotes withanolide MESH:D054358
1895 1430-1443 Chemical denotes withanolide A
1899 1491-1496 Gene denotes spike Gene:43740568
1900 1480-1490 Species denotes SARS–CoV–2 Tax:2697049
1901 1539-1552 Chemical denotes withanolide A
1908 2762-2768 Gene denotes PL-pro Gene:43740578
1909 2470-2475 Gene denotes spike Gene:43740568
1910 2770-2773 Gene denotes PDB Gene:5131
1911 2490-2493 Gene denotes PDB Gene:5131
1912 2461-2469 Species denotes SARS–CoV Tax:694009
1913 2751-2761 Species denotes SARS-CoV–2 Tax:2697049
1926 3185-3188 Gene denotes PC1 Gene:7163
1927 3190-3193 Gene denotes PC2 Gene:3854
1928 3198-3201 Gene denotes PC3 Gene:3853
1929 3277-3280 Gene denotes PC2 Gene:3854
1930 3285-3288 Gene denotes PC3 Gene:3853
1931 3605-3608 Gene denotes PC1 Gene:7163
1932 3610-3613 Gene denotes PC2 Gene:3854
1933 3618-3621 Gene denotes PC3 Gene:3853
1934 3016-3021 Gene denotes spike Gene:43740568
1935 3272-3275 Gene denotes PC1 Gene:7163
1936 3036-3039 Gene denotes PDB Gene:5131
1937 3007-3015 Species denotes SARS–CoV Tax:694009
1941 3863-3868 Gene denotes spike Gene:43740568
1942 3883-3886 Gene denotes PDB Gene:5131
1943 3854-3862 Species denotes SARS–CoV Tax:694009
1950 4613-4619 Gene denotes PL-pro Gene:43740578
1951 4621-4624 Gene denotes PDB Gene:5131
1952 4341-4344 Gene denotes PDB Gene:5131
1953 4315-4325 Species denotes SARS-CoV-2 Tax:2697049
1954 4602-4612 Species denotes SARS-CoV-2 Tax:2697049
1955 4360-4373 Chemical denotes withanolide A
1967 5033-5036 Gene denotes PC1 Gene:7163
1968 5038-5041 Gene denotes PC2 Gene:3854
1969 5046-5049 Gene denotes PC3 Gene:3853
1970 5125-5128 Gene denotes PC2 Gene:3854
1971 5133-5136 Gene denotes PC3 Gene:3853
1972 5453-5456 Gene denotes PC1 Gene:7163
1973 5458-5461 Gene denotes PC2 Gene:3854
1974 5466-5469 Gene denotes PC3 Gene:3853
1975 5120-5123 Gene denotes PC1 Gene:7163
1976 4884-4887 Gene denotes PDB Gene:5131
1977 4858-4868 Species denotes SARS-CoV-2 Tax:2697049
1981 5711-5716 Gene denotes spike Gene:43740568
1982 5731-5734 Gene denotes PDB Gene:5131
1983 5702-5710 Species denotes SARS-CoV Tax:694009

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T12 4192-4199 Phenotype denotes mol) (E http://purl.obolibrary.org/obo/HP_0003764
T13 6040-6047 Phenotype denotes mol) (E http://purl.obolibrary.org/obo/HP_0003764

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1016 0-5 Sentence denotes 3.11.
T1017 7-36 Sentence denotes Molecular dynamics simulation
T1018 37-158 Sentence denotes Figures 9 and 10, respectively, depict molecular simulation analysis of SARS-CoV-2 spike receptor-binding domain (PDB ID:
T1019 159-234 Sentence denotes 6M0J) bound with withanolide A and SARS-CoV-2 papain-like protease (PDB ID:
T1020 235-266 Sentence denotes 6W9C) bound with withanolide B.
T1021 267-352 Sentence denotes Both MD simulations showed an acceptable stability profile at a temperature of 300 K.
T1022 353-569 Sentence denotes Root mean square deviation (RMSD) is one of the most important fundamental properties to establish protein stability and its conformation to experimental structure (Kuzmanic & Zagrovic, 2010; Laskowski et al., 1997).
T1023 570-772 Sentence denotes RMSD is a measure of the deviation of the 3D or tertiary structure of a protein and is applied in order to get an insight into the stability of the protein in a biological system during a MD simulation.
T1024 773-1013 Sentence denotes SARS-CoV-2 spike receptor-binding domain-withanolide A complex displayed constant RMSDs (0.5–2.0 angstrom) of both protein side chains and Cα atoms from the initial structure (before equilibrium) throughout the 3 ns time scale (Figure 9.1).
T1025 1014-1241 Sentence denotes Similarly, SARS-CoV-2 papain-like protease-withanolide B complex also exhibited constant RMSDs (0.8–2.9 angstrom) of both protein side chains and Cα atoms from the initial structure throughout the 3 ns time scale (Figure 10.1).
T1026 1242-1355 Sentence denotes Figures 11.1–11.3 and 12.1–12.3, respectively depict MS dynamics analyses of SARS-CoV spike glycoprotein (PDB ID:
T1027 1356-1418 Sentence denotes 5WRG) with withanolide B and SARS-CoV-2 main protease (PDB ID:
T1028 1419-1444 Sentence denotes 6LU7) with withanolide A.
T1029 1445-1454 Sentence denotes Figure 9.
T1030 1456-1594 Sentence denotes Molecular simulation of SARS–CoV–2 spike receptor–binding domain bound (6M0J) with withanolide A using Playmolecule open server (Table 1).
T1031 1595-1682 Sentence denotes Figures 9.1–9.2, Tables 2–4 here corresponds to the tables of MD simulation statistics.
T1032 1683-1749 Sentence denotes RMSD values were obtained as a function of time obtained at 300 K.
T1033 1750-1798 Sentence denotes Values were calculated with the use of Cα atoms.
T1034 1799-1815 Sentence denotes Figures 9.3–9.4.
T1035 1816-1899 Sentence denotes Average RMSF values obtained as a function of amino acid sequence numbers at 300 K.
T1036 1900-1948 Sentence denotes Values were calculated with the use of Cα atoms.
T1037 1949-1959 Sentence denotes Figure 10.
T1038 1961-2071 Sentence denotes Molecular simulation of papain–like protease (6W9C–A chain) with withanolide B using Playmolecule open server.
T1039 2072-2161 Sentence denotes Figures 10.1–10.2, Tables 2–4 here corresponds to the tables of MD simulation statistics.
T1040 2162-2228 Sentence denotes RMSD values were obtained as a function of time obtained at 300 K.
T1041 2229-2277 Sentence denotes Values were calculated with the use of Cα atoms.
T1042 2278-2296 Sentence denotes Figures 10.3–10.4.
T1043 2297-2380 Sentence denotes Average RMSF values obtained as a function of amino acid sequence numbers at 300 K.
T1044 2381-2429 Sentence denotes Values were calculated with the use of Cα atoms.
T1045 2430-2442 Sentence denotes Figure 11.1.
T1046 2444-2497 Sentence denotes MD simulation of SARS–CoV spike glycoprotein (PDB ID:
T1047 2498-2777 Sentence denotes 5WRG) with withanolide B using LARMD online server. (A) Ligand–protein conformation, (B) RMSD of receptor and ligand (C) RMSD histogram of receptor (D) RMSD histogram of ligand (E) Radius of gyration—Rg value (F) Fraction of native contacts analysis of SARS-CoV–2 PL-pro (PDB ID:
T1048 2778-2985 Sentence denotes 6W9C) with withanolide B over a time frame of 4000 ps (4 ns) (G) RMSF value of each residue (H) B–factor value (changing from blue to red with increase in value) and (I) B–factor analysis of defined complex.
T1049 2986-2998 Sentence denotes Figure 11.2.
T1050 3000-3043 Sentence denotes PCA of SARS–CoV spike glycoprotein (PDB ID:
T1051 3044-3778 Sentence denotes 5WRG) with withanolide B (A) PCA results for Trajectory (B) Simple clustering in PC subspace(C) Table data showing residue–wise loadings for PC1, PC2 and PC3 and residue number at each position (D) Clustering dendogram based on PC1, PC2 and PC3 (E) Dynamical residue cross–correlation map; the correlated residues are in blue, anti–correlated residues are in red; the pairwise residues with higher correlated coefficient (>0.8) and with higher anti–correlated coefficient (≤0.4) are linked with light pink and light blue (Int_mod) (F) Residue–wise loadings for PC1, PC2 and PC3 (G) Table showing pairwise cross–correlation coefficients; higher correlated coefficient value is >0.8 and higher anti–correlated coefficient value is ≤0.4.
T1052 3779-3791 Sentence denotes Figure 11.3.
T1053 3793-3890 Sentence denotes Energy, hydrogen bond analysis and decomposition analysis of SARS–CoV spike glycoprotein (PDB ID:
T1054 3891-4283 Sentence denotes 5WRG) with withanolide B (A) MM/PB(GB)SA result consists of electrostatic energy (ELE), van der Waals contribution (VDW), total gas phase energy (GAS), non–polar and polar contributions to solvation (PBSOL/GBSOL) (B,C) Statistics of hydrogen bonds (D) energy decompose of protein–ligand complex (Kcal/mol) (E) Graphical representation of decompose result (F) Showing the heatmap of decompose.
T1055 4284-4296 Sentence denotes Figure 12.1.
T1056 4298-4348 Sentence denotes MD Simulation of SARS-CoV-2 main protease (PDB ID:
T1057 4349-4628 Sentence denotes 6LU7) with withanolide A using LARMD online server. (A) Ligand-protein conformation (B) RMSD of receptor and ligand (C) RMSD histogram of receptor (D) RMSD histogram of ligand (E) Radius of gyration- Rg value (F) Fraction of native contacts analysis of SARS-CoV-2 PL-pro (PDB ID:
T1058 4629-4836 Sentence denotes 6W9C) with withanolide A, over a time frame of 4000ps (4 ns) (G) RMSF value of each residue (H) B-factor value (changing from blue to red with increase in value) and (I) B-factor analysis of defined complex.
T1059 4837-4849 Sentence denotes Figure 12.2.
T1060 4851-4891 Sentence denotes PCA of SARS-CoV-2 main protease (PDB ID:
T1061 4892-5626 Sentence denotes 6LU7) with withanolide A (A) PCA results for trajectory (B) Simple clustering in PC subspace(C) Table data showing residue-wise loadings for PC1, PC2 and PC3 and residue number at each position (D) Clustering dendogram based on PC1, PC2 and PC3 (E) Dynamical residue cross-correlation map; the correlated residues are in blue, anti-correlated residues are in red; the pairwise residues with higher correlated coefficient (>0.8) and with higher anti-correlated coefficient (≤0.4) are linked with light pink and light blue (Int_mod) (F) Residue-wise loadings for PC1, PC2 and PC3 (G) Table showing pairwise cross-correlation coefficients; higher correlated coefficient value is >0.8 and higher anti-correlated coefficient value is ≤0.4.
T1062 5627-5639 Sentence denotes Figure 12.3.
T1063 5641-5738 Sentence denotes Energy, hydrogen bond analysis and decomposition analysis of SARS-CoV spike glycoprotein (PDB ID:
T1064 5739-6131 Sentence denotes 5WRG) with withanolide B (A) MM/PB(GB)SA result consists of electrostatic energy (ELE), van der Waals contribution (VDW), total gas phase energy (GAS), non-polar and polar contributions to solvation (PBSOL/GBSOL) (B,C) Statistics of hydrogen bonds (D) Energy decompose of protein–ligand complex (Kcal/mol) (E) Graphical representation of decompose result (F) Showing the heatmap of decompose.
T1065 6132-6228 Sentence denotes Vibrations around the equilibrium are not random, but depend on the local structure flexibility.
T1066 6229-6508 Sentence denotes In order to calculate the average fluctuation of all residues during simulations, the root mean square fluctuation (RMSF) of the Cα atoms of both target proteins were plotted from the primary structure of both proteins as a function of residue number (Kuzmanic & Zagrovic, 2010).
T1067 6509-6643 Sentence denotes The obtained patterns of RMSFs for both the proteins and ligands have been presented in Figures 11.1–11.3 and 12.1–12.3, respectively.