PMC:7219429 / 6466-8537
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T36 | 688-695 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T31 | 621-624 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
| T33 | 671-679 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T34 | 842-845 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T66 | 250-252 | http://purl.obolibrary.org/obo/CLO_0050510 | denotes | 18 |
| T67 | 486-488 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T68 | 520-525 | http://purl.obolibrary.org/obo/UBERON_0007688 | denotes | field |
| T69 | 703-704 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T70 | 774-775 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T71 | 994-999 | http://purl.obolibrary.org/obo/UBERON_0007688 | denotes | field |
| T72 | 1020-1021 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T73 | 1052-1053 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T74 | 1100-1101 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | Å |
| T75 | 1270-1272 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T76 | 1328-1330 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
| T77 | 1344-1346 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
| T78 | 1478-1480 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
| T79 | 1523-1525 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T80 | 1703-1704 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T97 | 312-315 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T98 | 486-488 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T99 | 571-574 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T100 | 688-695 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T101 | 755-759 | Chemical | denotes | drug | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T102 | 809-812 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T103 | 813-822 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T104 | 1168-1174 | Chemical | denotes | ligand | http://purl.obolibrary.org/obo/CHEBI_52214 |
| T105 | 1270-1272 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T106 | 1523-1525 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T52 | 0-264 | Sentence | denotes | Molecular modelling studies were performed using Hyperchem (http://www.hyper.com), Deep View/Swiss-Pdb viewer (https://spdbv.vital-it.ch) and Molegro Molecular viewer (http://molexus.io/molegro-molecular-viewer) as described previously [[16], [17], [18], [19],23]. |
| T53 | 265-374 | Sentence | denotes | Lennard-Jones parameters and atomic charges of ATM obtained from pdb file # 5UXD were checked with Hyperchem. |
| T54 | 375-547 | Sentence | denotes | The molecular modelling protocol consisted of docking, equilibration, and subsequent 50-ns molecular dynamics (MD) simulations with CHARMM force field [16,24] in Hyperchem. |
| T55 | 548-760 | Sentence | denotes | The starting point for ATM docking was done by manual positioning on the NTD and receptor-binding domain (RBD) surfaces of SARS-CoV-2 spike protein (chain A) with full consideration of the properties of the drug. |
| T56 | 761-868 | Sentence | denotes | In addition, a series of 20 randomly positioned ATM molecules covering the whole NTD surface were analysed. |
| T57 | 869-1139 | Sentence | denotes | Energy minimization of each system was then performed with the Polak-Ribière conjugate gradient algorithm, with CHARMM force field in Hyperchem, using a maximum of 3 × 105 steps, and a root-mean-square (RMS) gradient of 0.01 kcal. Å−1.mol−1 as the convergence condition. |
| T58 | 1140-1481 | Sentence | denotes | According to the validation ligand-binding protocol [25], the optimized docked structures were used as the initial structures for MD simulations with the following parameters: heat time 5 ps, run time 10 ps, step size 1 fs, starting temperature 0 K, simulation temperature 300 K, temperature step 30 K, bath relaxation time step size 0.1 ps. |
| T59 | 1482-1602 | Sentence | denotes | Each complex was submitted to 50-ns long MD trajectories, replicated three times, with convergent trajectories obtained. |
| T60 | 1603-1664 | Sentence | denotes | Frames were saved at 10 ns intervals for subsequent analysis. |
| T61 | 1665-1838 | Sentence | denotes | The final complex obtained with chain A was reintroduced in the trimeric spike structure (pdb file # 6VSB) with Molegro Molecular viewer and with Deep View Swiss-Pdb viewer. |
| T62 | 1839-1888 | Sentence | denotes | Similar results were obtained with both programs. |
| T63 | 1889-2002 | Sentence | denotes | The energies of interaction were extracted from the Ligand Energy Inspector function of Molegro Molecular viewer. |
| T64 | 2003-2071 | Sentence | denotes | Molecular volumes were calculated by the QSAR function of Hyperchem. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 221 | 682-687 | Gene | denotes | spike | Gene:43740568 |
| 222 | 1738-1743 | Gene | denotes | spike | Gene:43740568 |
| 223 | 1827-1830 | Gene | denotes | Pdb | Gene:5131 |
| 224 | 1755-1758 | Gene | denotes | pdb | Gene:5131 |
| 225 | 330-333 | Gene | denotes | pdb | Gene:5131 |
| 226 | 99-102 | Gene | denotes | Pdb | Gene:5131 |
| 227 | 671-681 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32405156-31431523-48151013 | 238-240 | 31431523 | denotes | 16 |
| 32405156-26915987-48151014 | 250-252 | 26915987 | denotes | 18 |
| 32405156-21756873-48151015 | 256-258 | 21756873 | denotes | 19 |
| 32405156-28205163-48151016 | 260-262 | 28205163 | denotes | 23 |
| 32405156-31431523-48151017 | 527-529 | 31431523 | denotes | 16 |
| 32405156-30525595-48151018 | 530-532 | 30525595 | denotes | 24 |
| 32405156-30236283-48151019 | 1193-1195 | 30236283 | denotes | 25 |
| T19862 | 238-240 | 31431523 | denotes | 16 |
| T59147 | 250-252 | 26915987 | denotes | 18 |
| T89313 | 256-258 | 21756873 | denotes | 19 |
| T99169 | 260-262 | 28205163 | denotes | 23 |
| T18657 | 527-529 | 31431523 | denotes | 16 |
| T88529 | 530-532 | 30525595 | denotes | 24 |
| T26528 | 1193-1195 | 30236283 | denotes | 25 |