PMC:7081066 / 3629-5135
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 138 | 36-41 | Gene | denotes | spike | Gene:43740568 |
| 139 | 409-414 | Gene | denotes | spike | Gene:43740568 |
| 140 | 350-355 | Gene | denotes | spike | Gene:43740568 |
| 141 | 55-65 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 142 | 87-90 | Species | denotes | CoV | Tax:11118 |
| 143 | 339-349 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 144 | 400-408 | Species | denotes | SARS-CoV | Tax:694009 |
| 145 | 467-470 | Species | denotes | CoV | Tax:11118 |
| 146 | 626-634 | Chemical | denotes | Hydrogen | MESH:D006859 |
| 147 | 755-760 | Chemical | denotes | water | MESH:D014867 |
| 148 | 928-933 | Chemical | denotes | water | MESH:D014867 |
| 149 | 1202-1208 | Disease | denotes | CHARMM |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T22 | 42-49 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T23 | 415-422 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T24 | 453-457 | Body_part | denotes | hand | http://purl.org/sig/ont/fma/fma9712 |
| T25 | 594-601 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T26 | 717-724 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T27 | 840-847 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
| T28 | 848-856 | Body_part | denotes | backbone | http://purl.org/sig/ont/fma/fma13478 |
| T29 | 948-955 | Body_part | denotes | protein | http://purl.org/sig/ont/fma/fma67257 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T1 | 453-457 | Body_part | denotes | hand | http://purl.obolibrary.org/obo/UBERON_0002398 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T21 | 55-63 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T22 | 339-347 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T23 | 400-408 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T26 | 747-748 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T27 | 753-754 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | Å |
| T28 | 988-990 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T29 | 1059-1061 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T30 | 1215-1220 | http://purl.obolibrary.org/obo/UBERON_0007688 | denotes | field |
| T31 | 1353-1355 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T21 | 42-49 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T22 | 415-422 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T23 | 594-601 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T24 | 626-634 | Chemical | denotes | Hydrogen | http://purl.obolibrary.org/obo/CHEBI_18276 |
| T25 | 635-640 | Chemical | denotes | atoms | http://purl.obolibrary.org/obo/CHEBI_33250 |
| T26 | 717-724 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T27 | 755-760 | Chemical | denotes | water | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T28 | 840-847 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T29 | 928-933 | Chemical | denotes | water | http://purl.obolibrary.org/obo/CHEBI_15377 |
| T30 | 934-943 | Chemical | denotes | molecules | http://purl.obolibrary.org/obo/CHEBI_25367 |
| T31 | 948-955 | Chemical | denotes | protein | http://purl.obolibrary.org/obo/CHEBI_36080 |
| T32 | 988-990 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T33 | 1059-1061 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T34 | 1353-1355 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T31 | 0-241 | Sentence | denotes | Homology structural models of viral spike protein from SARS-CoV-2 (QHO62112.1) and Bat-CoV (AAZ67052.1) were built by using the tools of the SWISS-MODEL modeling server and the DeepView/Swiss-PdbViewer 4.01 software (Arnold et al., 2006[1]). |
| T32 | 242-319 | Sentence | denotes | Several models were obtained and the quality of each structure was evaluated. |
| T33 | 320-439 | Sentence | denotes | The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). |
| T34 | 440-554 | Sentence | denotes | On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. |
| T35 | 555-625 | Sentence | denotes | These models were subjected to further protein structure optimization. |
| T36 | 626-712 | Sentence | denotes | Hydrogen atoms were added and the partial charges were assigned for energy refinement. |
| T37 | 713-765 | Sentence | denotes | The protein model was embedded in a 100 Å water box. |
| T38 | 766-956 | Sentence | denotes | Then, energy minimization was performed while applying constraints to the protein backbone to preserve global folding and optimizing the relative position of the water molecules and protein. |
| T39 | 957-1054 | Sentence | denotes | The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). |
| T40 | 1055-1201 | Sentence | denotes | All MD simulations described in this study were performed with NAMD 2.12 (Phillips et al., 2005[10]), Vega ZZ 3.1.0.21 (Pedretti et al., 2004[9]). |
| T41 | 1202-1287 | Sentence | denotes | CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. |
| T42 | 1288-1368 | Sentence | denotes | The obtained structures represent the lowest energy frame of the MD simulations. |
| T43 | 1369-1506 | Sentence | denotes | The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]). |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32210742-16301204-29811227 | 237-238 | 16301204 | denotes | 1 |
| 32210742-31762727-29811228 | 1050-1051 | 31762727 | denotes | 8 |
| 32210742-16222654-29811229 | 1151-1153 | 16222654 | denotes | 10 |
| 32210742-15368917-29811230 | 1197-1198 | 15368917 | denotes | 9 |
| 32210742-19575467-29811231 | 1250-1252 | 19575467 | denotes | 14 |
| 32210742-17517781-29811232 | 1451-1453 | 17517781 | denotes | 17 |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32210742-16301204-29811227 | 237-238 | 16301204 | denotes | 1 |
| 32210742-31762727-29811228 | 1050-1051 | 31762727 | denotes | 8 |
| 32210742-16222654-29811229 | 1151-1153 | 16222654 | denotes | 10 |
| 32210742-15368917-29811230 | 1197-1198 | 15368917 | denotes | 9 |
| 32210742-19575467-29811231 | 1250-1252 | 19575467 | denotes | 14 |
| 32210742-17517781-29811232 | 1451-1453 | 17517781 | denotes | 17 |