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LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T46","span":{"begin":536,"end":544},"obj":"Disease"}],"attributes":[{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"2.1.2. Ligand preparations\nThe SDF structures of GTP, remdesivir, and selected hundred polyphenols (see Table S1 in Supplementary Information) were retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) (Kim et al., 2019). The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).\nTable 1. Binding energy (kcal/mol) of the natural polyphenols along with the control compounds (GTP and remdesivir) against RdRp of the SARS-CoV-2 (PDB ID: 6M71) by molecular docking study.\nS. No. Compound Name Binding energy (kcal/mol) S. No. Compound Name Binding energy (kcal/mol)\n1 TF3 −9.9 52 Cyanidin −6.3\n2 TF2b −9.6 53 Daidzein −6.3\n3 TF1 −9.6 54 Glycitein −6.3\n4 TF2a −9.3 55 Wogonin −6.3\n5 Hesperidin −8.8 56 Phloretin −6.3\n6 EGCG −7.3 57 Catechin −6.2\n7 Myricetin −7.2 58 Urolithin B −6.2\n8 Quercetagetin −7.0 59 Angolensin −6.2\n9 Quercetin −6.9 60 Pinosylvin −6.2\n10 Curcumin −6.9 61 Formononetin −6.2\n11 Dihydrorobinetin −6.8 62 Liquiritigenin −6.2\n12 Peonidin −6.8 63 Prunetin −6.2\n13 Fisetin −6.8 64 Alpinetin −6.2\n14 Robinetin −6.7 65 Biochanin A −6.2\n15 5-Deoxygalangin −6.7 66 Rhapontigenin −6.1\n16 Kaempferol −6.7 67 Genistein −6.1\n17 Scutellarein −6.7 68 Chrysin −6.1\n18 (-)-Epicatechin −6.7 69 6-Hydroxyflavone −6.1\n19 Purpurin −6.7 70 Equol −6.1\n20 Isorhamnetin −6.7 71 Piceatannol −6.1\n21 Tricetin −6.6 72 Isorhapontigenin −6.0\n22 Gossypetin −6.6 73 Resveratrol −5.8\n23 Norathyriol −6.6 74 Danshensu −5.7\n24 Coumestrol −6.6 75 Eugenin −5.6\n25 Isosakuranetin −6.6 76 Sinapic acid −5.5\n26 Pectolinarigenin −6.6 77 Pterostilbene −5.5\n27 Tangeritin −6.6 78 Ferulic acid −5.4\n28 Nobiletin −6.6 79 Caffeic acid −5.4\n29 Pratensein −6.6 80 Isoferulic acid −5.4\n30 Hispidulin −6.6 81 Dihydrocaffeic acid −5.4\n31 Baicalein −6.5 82 Gentisic acid −5.3\n32 Apigenin −6.5 83 Pyrogallol −5.3\n33 Morin −6.5 84 4-Hydroxycinnamic acid −5.2\n34 Urolithin A −6.5 85 Resacetophenone −5.2\n35 Acacetin −6.5 86 Salicyclic acid −5.1\n36 Pelargonidin −6.5 87 Syringic acid −5.1\n37 Irilone −6.5 88 2-Hydroxybenzoic acid −5.1\n38 Naringenin −6.5 89 Gallic acid −5.0\n39 Pinocembrin −6.5 90 3-Hydroxybenzoic acid −5.0\n40 Kaempferide −6.5 91 4-Hydroxybenzoic acid −5.0\n41 Malvidin −6.5 92 Vanillin −5.0\n42 Luteolin −6.4 93 p-Coumeric acid −4.9\n43 Dalbergin −6.4 94 Vanillic acid −4.8\n44 Butein −6.4 95 Paeonol −4.8\n45 Biochanin A (1-) −6.4 96 Cinnamic acid −4.7\n46 Fustin −6.4 97 Protocatechuic acid −4.6\n47 5-Hydroxyflavone −6.4 98 4-Ethylphenol −4.5\n48 Pinostrobin −6.4 99 Catechol −4.5\n49 Pinobanksin −6.4 100 Tyrosol −4.5\n50 Datiscetin −6.3 101 GTP −7.9\n51 Galangin −6.3 102 Remdesivir −7.7"}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PubTator

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T3","span":{"begin":764,"end":767},"obj":"GlycoEpitope"}],"attributes":[{"id":"A3","pred":"glyco_epitope_db_id","subj":"T3","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"2.1.2. Ligand preparations\nThe SDF structures of GTP, remdesivir, and selected hundred polyphenols (see Table S1 in Supplementary Information) were retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) (Kim et al., 2019). The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).\nTable 1. Binding energy (kcal/mol) of the natural polyphenols along with the control compounds (GTP and remdesivir) against RdRp of the SARS-CoV-2 (PDB ID: 6M71) by molecular docking study.\nS. No. Compound Name Binding energy (kcal/mol) S. No. Compound Name Binding energy (kcal/mol)\n1 TF3 −9.9 52 Cyanidin −6.3\n2 TF2b −9.6 53 Daidzein −6.3\n3 TF1 −9.6 54 Glycitein −6.3\n4 TF2a −9.3 55 Wogonin −6.3\n5 Hesperidin −8.8 56 Phloretin −6.3\n6 EGCG −7.3 57 Catechin −6.2\n7 Myricetin −7.2 58 Urolithin B −6.2\n8 Quercetagetin −7.0 59 Angolensin −6.2\n9 Quercetin −6.9 60 Pinosylvin −6.2\n10 Curcumin −6.9 61 Formononetin −6.2\n11 Dihydrorobinetin −6.8 62 Liquiritigenin −6.2\n12 Peonidin −6.8 63 Prunetin −6.2\n13 Fisetin −6.8 64 Alpinetin −6.2\n14 Robinetin −6.7 65 Biochanin A −6.2\n15 5-Deoxygalangin −6.7 66 Rhapontigenin −6.1\n16 Kaempferol −6.7 67 Genistein −6.1\n17 Scutellarein −6.7 68 Chrysin −6.1\n18 (-)-Epicatechin −6.7 69 6-Hydroxyflavone −6.1\n19 Purpurin −6.7 70 Equol −6.1\n20 Isorhamnetin −6.7 71 Piceatannol −6.1\n21 Tricetin −6.6 72 Isorhapontigenin −6.0\n22 Gossypetin −6.6 73 Resveratrol −5.8\n23 Norathyriol −6.6 74 Danshensu −5.7\n24 Coumestrol −6.6 75 Eugenin −5.6\n25 Isosakuranetin −6.6 76 Sinapic acid −5.5\n26 Pectolinarigenin −6.6 77 Pterostilbene −5.5\n27 Tangeritin −6.6 78 Ferulic acid −5.4\n28 Nobiletin −6.6 79 Caffeic acid −5.4\n29 Pratensein −6.6 80 Isoferulic acid −5.4\n30 Hispidulin −6.6 81 Dihydrocaffeic acid −5.4\n31 Baicalein −6.5 82 Gentisic acid −5.3\n32 Apigenin −6.5 83 Pyrogallol −5.3\n33 Morin −6.5 84 4-Hydroxycinnamic acid −5.2\n34 Urolithin A −6.5 85 Resacetophenone −5.2\n35 Acacetin −6.5 86 Salicyclic acid −5.1\n36 Pelargonidin −6.5 87 Syringic acid −5.1\n37 Irilone −6.5 88 2-Hydroxybenzoic acid −5.1\n38 Naringenin −6.5 89 Gallic acid −5.0\n39 Pinocembrin −6.5 90 3-Hydroxybenzoic acid −5.0\n40 Kaempferide −6.5 91 4-Hydroxybenzoic acid −5.0\n41 Malvidin −6.5 92 Vanillin −5.0\n42 Luteolin −6.4 93 p-Coumeric acid −4.9\n43 Dalbergin −6.4 94 Vanillic acid −4.8\n44 Butein −6.4 95 Paeonol −4.8\n45 Biochanin A (1-) −6.4 96 Cinnamic acid −4.7\n46 Fustin −6.4 97 Protocatechuic acid −4.6\n47 5-Hydroxyflavone −6.4 98 4-Ethylphenol −4.5\n48 Pinostrobin −6.4 99 Catechol −4.5\n49 Pinobanksin −6.4 100 Tyrosol −4.5\n50 Datiscetin −6.3 101 GTP −7.9\n51 Galangin −6.3 102 Remdesivir −7.7"}

LitCovid-sentences

2_test

{"project":"2_test","denotations":[{"id":"32720577-30371825-56195102","span":{"begin":234,"end":238},"obj":"30371825"},{"id":"32720577-15264254-56195103","span":{"begin":392,"end":396},"obj":"15264254"}],"text":"2.1.2. Ligand preparations\nThe SDF structures of GTP, remdesivir, and selected hundred polyphenols (see Table S1 in Supplementary Information) were retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) (Kim et al., 2019). The compounds were converted into PDB format, and conformational energies of all the compounds were minimized by using UCSF Chimera (Pettersen et al., 2004).\nTable 1. Binding energy (kcal/mol) of the natural polyphenols along with the control compounds (GTP and remdesivir) against RdRp of the SARS-CoV-2 (PDB ID: 6M71) by molecular docking study.\nS. No. Compound Name Binding energy (kcal/mol) S. No. Compound Name Binding energy (kcal/mol)\n1 TF3 −9.9 52 Cyanidin −6.3\n2 TF2b −9.6 53 Daidzein −6.3\n3 TF1 −9.6 54 Glycitein −6.3\n4 TF2a −9.3 55 Wogonin −6.3\n5 Hesperidin −8.8 56 Phloretin −6.3\n6 EGCG −7.3 57 Catechin −6.2\n7 Myricetin −7.2 58 Urolithin B −6.2\n8 Quercetagetin −7.0 59 Angolensin −6.2\n9 Quercetin −6.9 60 Pinosylvin −6.2\n10 Curcumin −6.9 61 Formononetin −6.2\n11 Dihydrorobinetin −6.8 62 Liquiritigenin −6.2\n12 Peonidin −6.8 63 Prunetin −6.2\n13 Fisetin −6.8 64 Alpinetin −6.2\n14 Robinetin −6.7 65 Biochanin A −6.2\n15 5-Deoxygalangin −6.7 66 Rhapontigenin −6.1\n16 Kaempferol −6.7 67 Genistein −6.1\n17 Scutellarein −6.7 68 Chrysin −6.1\n18 (-)-Epicatechin −6.7 69 6-Hydroxyflavone −6.1\n19 Purpurin −6.7 70 Equol −6.1\n20 Isorhamnetin −6.7 71 Piceatannol −6.1\n21 Tricetin −6.6 72 Isorhapontigenin −6.0\n22 Gossypetin −6.6 73 Resveratrol −5.8\n23 Norathyriol −6.6 74 Danshensu −5.7\n24 Coumestrol −6.6 75 Eugenin −5.6\n25 Isosakuranetin −6.6 76 Sinapic acid −5.5\n26 Pectolinarigenin −6.6 77 Pterostilbene −5.5\n27 Tangeritin −6.6 78 Ferulic acid −5.4\n28 Nobiletin −6.6 79 Caffeic acid −5.4\n29 Pratensein −6.6 80 Isoferulic acid −5.4\n30 Hispidulin −6.6 81 Dihydrocaffeic acid −5.4\n31 Baicalein −6.5 82 Gentisic acid −5.3\n32 Apigenin −6.5 83 Pyrogallol −5.3\n33 Morin −6.5 84 4-Hydroxycinnamic acid −5.2\n34 Urolithin A −6.5 85 Resacetophenone −5.2\n35 Acacetin −6.5 86 Salicyclic acid −5.1\n36 Pelargonidin −6.5 87 Syringic acid −5.1\n37 Irilone −6.5 88 2-Hydroxybenzoic acid −5.1\n38 Naringenin −6.5 89 Gallic acid −5.0\n39 Pinocembrin −6.5 90 3-Hydroxybenzoic acid −5.0\n40 Kaempferide −6.5 91 4-Hydroxybenzoic acid −5.0\n41 Malvidin −6.5 92 Vanillin −5.0\n42 Luteolin −6.4 93 p-Coumeric acid −4.9\n43 Dalbergin −6.4 94 Vanillic acid −4.8\n44 Butein −6.4 95 Paeonol −4.8\n45 Biochanin A (1-) −6.4 96 Cinnamic acid −4.7\n46 Fustin −6.4 97 Protocatechuic acid −4.6\n47 5-Hydroxyflavone −6.4 98 4-Ethylphenol −4.5\n48 Pinostrobin −6.4 99 Catechol −4.5\n49 Pinobanksin −6.4 100 Tyrosol −4.5\n50 Datiscetin −6.3 101 GTP −7.9\n51 Galangin −6.3 102 Remdesivir −7.7"}