PMC:7605337 / 18007-18568
Annnotations
LitCovid-PD-FMA-UBERON
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. 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. 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-PD-MONDO
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. 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. 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-PD-CLO
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. 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. 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-PD-CHEBI
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. 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. 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-sentences
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. 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. 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
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. 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. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°.