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PMC:7544943 / 11747-13050 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T14 61-68 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T37 509-517 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 622-630 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 700-708 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 724-732 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T47 231-234 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T48 272-273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 302-303 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 408-409 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 425-426 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T52 432-433 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T53 439-440 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T54 526-527 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55 548-549 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T56 552-554 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T57 555-556 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T58 562-563 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T59 969-975 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T60 1043-1046 http://purl.obolibrary.org/obo/CLO_0050167 denotes LLC
T61 1292-1295 http://purl.obolibrary.org/obo/CLO_0050167 denotes LLC

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
256 711-715 Gene denotes Mpro Gene:8673700
257 520-524 Gene denotes Mpro Gene:8673700
258 509-519 Species denotes SARS-CoV-2 Tax:2697049
259 622-632 Species denotes SARS-CoV-2 Tax:2697049
260 700-710 Species denotes SARS-CoV-2 Tax:2697049
261 724-734 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T113 0-4 Sentence denotes 2.3.
T114 6-29 Sentence denotes Molecular docking study
T115 30-167 Sentence denotes The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott & Olson, 2010).
T116 168-263 Sentence denotes AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy.
T117 264-407 Sentence denotes It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space.
T118 408-525 Sentence denotes A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro.
T119 526-642 Sentence denotes A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro.
T120 643-820 Sentence denotes The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results.
T121 821-912 Sentence denotes The docked poses were ranked as per their binding affinities at the end of the docking run.
T122 913-1054 Sentence denotes The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017).
T123 1055-1165 Sentence denotes The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005).
T124 1166-1303 Sentence denotes The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017).

2_test

Id Subject Object Predicate Lexical cue
32938313-19499576-56197380 161-165 19499576 denotes 2010