PMC:7219429 / 6417-8537
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T36 | 737-744 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T31 | 670-673 | Disease | denotes | NTD | http://purl.obolibrary.org/obo/MONDO_0008449|http://purl.obolibrary.org/obo/MONDO_0018075 |
| T33 | 720-728 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T34 | 891-894 | 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 | 299-301 | http://purl.obolibrary.org/obo/CLO_0050510 | denotes | 18 |
| T67 | 535-537 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T68 | 569-574 | http://purl.obolibrary.org/obo/UBERON_0007688 | denotes | field |
| T69 | 752-753 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T70 | 823-824 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T71 | 1043-1048 | http://purl.obolibrary.org/obo/UBERON_0007688 | denotes | field |
| T72 | 1069-1070 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T73 | 1101-1102 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T74 | 1149-1150 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | Å |
| T75 | 1319-1321 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T76 | 1377-1379 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
| T77 | 1393-1395 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
| T78 | 1527-1529 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
| T79 | 1572-1574 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T80 | 1752-1753 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T97 | 361-364 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T98 | 535-537 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T99 | 620-623 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T100 | 737-744 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T101 | 804-808 | Chemical | denotes | drug | http://purl.obolibrary.org/obo/CHEBI_23888 |
| T102 | 858-861 | Chemical | denotes | ATM | http://purl.obolibrary.org/obo/CHEBI_2955 |
| T103 | 862-871 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T104 | 1217-1223 | Chemical | denotes | ligand | http://purl.obolibrary.org/obo/CHEBI_52214 |
| T105 | 1319-1321 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T106 | 1572-1574 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T51 | 0-48 | Sentence | denotes | 2.2 Molecular modelling and visualization tools |
| T52 | 49-313 | 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 | 314-423 | Sentence | denotes | Lennard-Jones parameters and atomic charges of ATM obtained from pdb file # 5UXD were checked with Hyperchem. |
| T54 | 424-596 | 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 | 597-809 | 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 | 810-917 | Sentence | denotes | In addition, a series of 20 randomly positioned ATM molecules covering the whole NTD surface were analysed. |
| T57 | 918-1188 | 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 | 1189-1530 | 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 | 1531-1651 | Sentence | denotes | Each complex was submitted to 50-ns long MD trajectories, replicated three times, with convergent trajectories obtained. |
| T60 | 1652-1713 | Sentence | denotes | Frames were saved at 10 ns intervals for subsequent analysis. |
| T61 | 1714-1887 | 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 | 1888-1937 | Sentence | denotes | Similar results were obtained with both programs. |
| T63 | 1938-2051 | Sentence | denotes | The energies of interaction were extracted from the Ligand Energy Inspector function of Molegro Molecular viewer. |
| T64 | 2052-2120 | 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 | 731-736 | Gene | denotes | spike | Gene:43740568 |
| 222 | 1787-1792 | Gene | denotes | spike | Gene:43740568 |
| 223 | 1876-1879 | Gene | denotes | Pdb | Gene:5131 |
| 224 | 1804-1807 | Gene | denotes | pdb | Gene:5131 |
| 225 | 379-382 | Gene | denotes | pdb | Gene:5131 |
| 226 | 148-151 | Gene | denotes | Pdb | Gene:5131 |
| 227 | 720-730 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32405156-31431523-48151013 | 287-289 | 31431523 | denotes | 16 |
| 32405156-26915987-48151014 | 299-301 | 26915987 | denotes | 18 |
| 32405156-21756873-48151015 | 305-307 | 21756873 | denotes | 19 |
| 32405156-28205163-48151016 | 309-311 | 28205163 | denotes | 23 |
| 32405156-31431523-48151017 | 576-578 | 31431523 | denotes | 16 |
| 32405156-30525595-48151018 | 579-581 | 30525595 | denotes | 24 |
| 32405156-30236283-48151019 | 1242-1244 | 30236283 | denotes | 25 |
| T19862 | 287-289 | 31431523 | denotes | 16 |
| T59147 | 299-301 | 26915987 | denotes | 18 |
| T89313 | 305-307 | 21756873 | denotes | 19 |
| T99169 | 309-311 | 28205163 | denotes | 23 |
| T18657 | 576-578 | 31431523 | denotes | 16 |
| T88529 | 579-581 | 30525595 | denotes | 24 |
| T26528 | 1242-1244 | 30236283 | denotes | 25 |