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PMC:7544943 / 11777-13050 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T14 31-38 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T37 479-487 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 592-600 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 670-678 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 694-702 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T47 201-204 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T48 242-243 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 272-273 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 378-379 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T51 395-396 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T52 402-403 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T53 409-410 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T54 496-497 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T55 518-519 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T56 522-524 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T57 525-526 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T58 532-533 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T59 939-945 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T60 1013-1016 http://purl.obolibrary.org/obo/CLO_0050167 denotes LLC
T61 1262-1265 http://purl.obolibrary.org/obo/CLO_0050167 denotes LLC

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
256 681-685 Gene denotes Mpro Gene:8673700
257 490-494 Gene denotes Mpro Gene:8673700
258 479-489 Species denotes SARS-CoV-2 Tax:2697049
259 592-602 Species denotes SARS-CoV-2 Tax:2697049
260 670-680 Species denotes SARS-CoV-2 Tax:2697049
261 694-704 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T115 0-137 Sentence denotes The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott & Olson, 2010).
T116 138-233 Sentence denotes AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy.
T117 234-377 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 378-495 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 496-612 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 613-790 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 791-882 Sentence denotes The docked poses were ranked as per their binding affinities at the end of the docking run.
T122 883-1024 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 1025-1135 Sentence denotes The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005).
T124 1136-1273 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 131-135 19499576 denotes 2010