PMC:7605337 / 16430-18568
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T48 | 1788-1796 | Body_part | denotes | backbone | http://purl.org/sig/ont/fma/fma13478 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T107 | 115-119 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T108 | 125-134 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T109 | 493-497 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T110 | 503-512 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T111 | 1879-1883 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T112 | 1892-1901 | Disease | denotes | nCOV-2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T110 | 415-416 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T111 | 822-823 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T112 | 1103-1105 | http://purl.obolibrary.org/obo/CLO_0007622 | denotes | MD |
| T113 | 1232-1235 | http://purl.obolibrary.org/obo/CLO_0003078 | denotes | FEL |
| T114 | 1809-1810 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T115 | 1983-1984 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T116 | 1989-1991 | http://purl.obolibrary.org/obo/CLO_0008491 | denotes | ps |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T65 | 253-256 | Chemical | denotes | PCA | http://purl.obolibrary.org/obo/CHEBI_36751|http://purl.obolibrary.org/obo/CHEBI_62248 |
| T67 | 678-683 | Chemical | denotes | atoms | http://purl.obolibrary.org/obo/CHEBI_33250 |
| T68 | 1103-1105 | Chemical | denotes | MD | http://purl.obolibrary.org/obo/CHEBI_74699 |
| T69 | 1800-1805 | Chemical | denotes | atoms | http://purl.obolibrary.org/obo/CHEBI_33250 |
| T70 | 2007-2015 | Chemical | denotes | Hydrogen | http://purl.obolibrary.org/obo/CHEBI_18276 |
| T71 | 2111-2116 | Chemical | denotes | donor | http://purl.obolibrary.org/obo/CHEBI_17891 |
| T72 | 2121-2129 | Chemical | denotes | acceptor | http://purl.obolibrary.org/obo/CHEBI_15339 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T5 | 341-354 | http://purl.obolibrary.org/obo/GO_0006412 | denotes | translational |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T84 | 0-40 | Sentence | denotes | Gibbs Free Energy and Correlated Motions |
| T85 | 41-447 | Sentence | denotes | The last 400 ns of simulation was used to explore the dominant motions in SARS-COV, nCOV-2019 and the mutations with extended simulation, and last 200 ns for all other mutants using principal component analysis (PCA) as part of the quasiharmonic analysis method.44 For this method the rotational and translational motions of RBD of all systems were eliminated by fitting to a reference (crystal) structure. |
| T86 | 448-691 | Sentence | denotes | Next, 4000 snapshots from the last 400 ns of SARS-COV, nCOV-2019 and mutations with extended simulation time, and 2000 snapshots from last 200 ns of all other mutant systems were taken to generate the covariance matrix between Cα atoms of RBD. |
| T87 | 692-778 | Sentence | denotes | In the mutant systems with production run, the last 400 ns was used for this analysis. |
| T88 | 779-1112 | Sentence | denotes | Diagonalization of this matrix resulted in a diagonal matrix of eigenvalues and their corresponding eigenvectors.43,45 The first eigenvector which indicate the first principal component was used to visualize the dominant global motions of all complexes through porcupine plots using the (PorcupinePlot.tcl) script in visual MD (VMD). |
| T89 | 1113-1215 | Sentence | denotes | The principal components were used to calculate and plot the approximate free energy landscape (aFEL). |
| T90 | 1216-1576 | Sentence | denotes | We refer to the FEL produced by this approach to be approximate in that the ensemble with respect to the first few PC’s (lowest frequency quasiharmonic modes) is not close to convergence, but the analysis can still provide valuable information and insight. g_sham, g_covar, and g_anaeig functions in GROMACS35 were used to obtain principal components and aFEL. |
| T91 | 1577-1828 | Sentence | denotes | The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. |
| T92 | 1829-2006 | Sentence | denotes | The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. |
| T93 | 2007-2138 | Sentence | denotes | Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°. |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 420 | 115-123 | Species | denotes | SARS-COV | Tax:694009 |
| 421 | 125-129 | Species | denotes | nCOV | Tax:2697049 |
| 422 | 493-501 | Species | denotes | SARS-COV | Tax:694009 |
| 423 | 503-507 | Species | denotes | nCOV | Tax:2697049 |
| 424 | 1096-1105 | Disease | denotes | visual MD | MESH:D009436 |
| 425 | 1107-1110 | Disease | denotes | VMD | |
| 427 | 1516-1523 | Gene | denotes | GROMACS | Gene:4082 |
| 434 | 1879-1887 | Species | denotes | SARS-COV | Tax:694009 |
| 435 | 1892-1896 | Species | denotes | nCOV | Tax:2697049 |
| 436 | 1716-1720 | Chemical | denotes | DCCM | |
| 437 | 2007-2015 | Chemical | denotes | Hydrogen | MESH:D006859 |
| 438 | 1788-1805 | Disease | denotes | backbone Cα atoms | |
| 439 | 2039-2042 | Disease | denotes | VMD |