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PMC:7081066 / 3224-5975 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
122 240-245 Gene denotes spike Gene:43740568
123 342-347 Gene denotes spike Gene:43740568
124 263-272 Species denotes SARS-CoV2 Tax:2697049
125 371-376 Gene denotes spike Gene:43740568
138 441-446 Gene denotes spike Gene:43740568
139 814-819 Gene denotes spike Gene:43740568
140 755-760 Gene denotes spike Gene:43740568
141 460-470 Species denotes SARS-CoV-2 Tax:2697049
142 492-495 Species denotes CoV Tax:11118
143 744-754 Species denotes SARS-CoV-2 Tax:2697049
144 805-813 Species denotes SARS-CoV Tax:694009
145 872-875 Species denotes CoV Tax:11118
146 1031-1039 Chemical denotes Hydrogen MESH:D006859
147 1160-1165 Chemical denotes water MESH:D014867
148 1333-1338 Chemical denotes water MESH:D014867
149 1607-1613 Disease denotes CHARMM
159 1994-1998 Gene denotes ACE2 Gene:59272
160 2270-2274 Gene denotes ACE2 Gene:59272
161 2409-2414 Gene denotes spike Gene:43740568
162 2438-2442 Gene denotes ACE2 Gene:59272
163 2260-2265 Gene denotes spike Gene:43740568
164 2099-2104 Gene denotes spike Gene:43740568
165 1968-1973 Gene denotes spike Gene:43740568
166 1959-1967 Species denotes SARS-CoV Tax:694009
167 2088-2098 Species denotes SARS-CoV-2 Tax:2697049

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T17 246-253 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T18 296-303 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T19 348-355 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T20 377-384 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T21 388-395 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T22 447-454 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T23 820-827 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T24 858-862 Body_part denotes hand http://purl.org/sig/ont/fma/fma9712
T25 999-1006 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T26 1122-1129 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T27 1245-1252 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T28 1253-1261 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T29 1353-1360 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T30 1913-1920 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T31 1921-1928 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T32 2040-2047 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T33 2118-2125 Body_part denotes Protein http://purl.org/sig/ont/fma/fma67257
T34 2415-2422 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 858-862 Body_part denotes hand http://purl.obolibrary.org/obo/UBERON_0002398

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T19 263-267 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T20 337-341 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T21 460-468 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 744-752 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T23 805-813 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T24 1959-1967 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 2088-2096 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T26 1152-1153 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 1158-1159 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T28 1393-1395 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T29 1464-1466 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T30 1620-1625 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T31 1758-1760 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T32 2377-2378 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T33 2501-2503 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T16 246-253 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T17 296-303 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T18 348-355 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T19 377-384 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T20 388-395 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T21 447-454 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T22 820-827 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T23 999-1006 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24 1031-1039 Chemical denotes Hydrogen http://purl.obolibrary.org/obo/CHEBI_18276
T25 1040-1045 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T26 1122-1129 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T27 1160-1165 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T28 1245-1252 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T29 1333-1338 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T30 1339-1348 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T31 1353-1360 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T32 1393-1395 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T33 1464-1466 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T34 1758-1760 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T35 1913-1920 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T36 1921-1928 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T37 2040-2047 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T38 2118-2125 Chemical denotes Protein http://purl.obolibrary.org/obo/CHEBI_16541
T39 2401-2407 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T40 2415-2422 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T26 0-21 Sentence denotes Materials and Methods
T27 23-40 Sentence denotes Sequence analysis
T28 41-178 Sentence denotes Sequences analyzed were individually retrieved from GenBank (accession numbers are shown in the phylogenetic tree, see Figure 1(Fig. 1)).
T29 179-386 Sentence denotes The sequence used for the modeling process and construct the spike protein model of SARS-CoV2 were obtained from the protein database and correspond to 6ACC (SARS spike protein) and 6ACD (Bat-spike protein).
T30 388-404 Sentence denotes Protein modeling
T31 405-646 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 647-724 Sentence denotes Several models were obtained and the quality of each structure was evaluated.
T33 725-844 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 845-959 Sentence denotes On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD.
T35 960-1030 Sentence denotes These models were subjected to further protein structure optimization.
T36 1031-1117 Sentence denotes Hydrogen atoms were added and the partial charges were assigned for energy refinement.
T37 1118-1170 Sentence denotes The protein model was embedded in a 100 Å water box.
T38 1171-1361 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 1362-1459 Sentence denotes The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]).
T40 1460-1606 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 1607-1692 Sentence denotes CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used.
T42 1693-1773 Sentence denotes The obtained structures represent the lowest energy frame of the MD simulations.
T43 1774-1911 Sentence denotes The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).
T44 1913-1936 Sentence denotes Protein-protein docking
T45 1937-2058 Sentence denotes Crystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank.
T46 2059-2117 Sentence denotes Also, the homology model for SARS-CoV-2 spike was assayed.
T47 2118-2173 Sentence denotes Protein preparation was carried out as described above.
T48 2174-2323 Sentence denotes Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking.
T49 2324-2506 Sentence denotes This process was performed through two steps; first, a blind docking between ligand (spike protein) and receptor (ACE2) was performed using Z-dock software (Pierce et al., 2014[11]).
T50 2507-2630 Sentence denotes Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]).
T51 2631-2751 Sentence denotes Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex.

MyTest

Id Subject Object Predicate Lexical cue
32210742-16301204-29811227 642-643 16301204 denotes 1
32210742-31762727-29811228 1455-1456 31762727 denotes 8
32210742-16222654-29811229 1556-1558 16222654 denotes 10
32210742-15368917-29811230 1602-1603 15368917 denotes 9
32210742-19575467-29811231 1655-1657 19575467 denotes 14
32210742-17517781-29811232 1856-1858 17517781 denotes 17
32210742-24532726-29811233 2501-2503 24532726 denotes 11
32210742-27503228-29811234 2625-2627 27503228 denotes 19

2_test

Id Subject Object Predicate Lexical cue
32210742-16301204-29811227 642-643 16301204 denotes 1
32210742-31762727-29811228 1455-1456 31762727 denotes 8
32210742-16222654-29811229 1556-1558 16222654 denotes 10
32210742-15368917-29811230 1602-1603 15368917 denotes 9
32210742-19575467-29811231 1655-1657 19575467 denotes 14
32210742-17517781-29811232 1856-1858 17517781 denotes 17
32210742-24532726-29811233 2501-2503 24532726 denotes 11
32210742-27503228-29811234 2625-2627 27503228 denotes 19