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LitCovid-PubTator

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":858,"end":862},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0002398"}],"text":"Materials and Methods\n\nSequence analysis\nSequences analyzed were individually retrieved from GenBank (accession numbers are shown in the phylogenetic tree, see Figure 1(Fig. 1)). 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).\n\nProtein modeling\nHomology 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]). Several models were obtained and the quality of each structure was evaluated. The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. These models were subjected to further protein structure optimization. Hydrogen atoms were added and the partial charges were assigned for energy refinement. The protein model was embedded in a 100 Å water box. 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. The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). 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]). CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. The obtained structures represent the lowest energy frame of the MD simulations. The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).\n\nProtein-protein docking\nCrystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. 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]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T19","span":{"begin":263,"end":267},"obj":"Disease"},{"id":"T20","span":{"begin":337,"end":341},"obj":"Disease"},{"id":"T21","span":{"begin":460,"end":468},"obj":"Disease"},{"id":"T22","span":{"begin":744,"end":752},"obj":"Disease"},{"id":"T23","span":{"begin":805,"end":813},"obj":"Disease"},{"id":"T24","span":{"begin":1959,"end":1967},"obj":"Disease"},{"id":"T25","span":{"begin":2088,"end":2096},"obj":"Disease"}],"attributes":[{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A23","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Materials and Methods\n\nSequence analysis\nSequences analyzed were individually retrieved from GenBank (accession numbers are shown in the phylogenetic tree, see Figure 1(Fig. 1)). 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).\n\nProtein modeling\nHomology 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]). Several models were obtained and the quality of each structure was evaluated. The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. These models were subjected to further protein structure optimization. Hydrogen atoms were added and the partial charges were assigned for energy refinement. The protein model was embedded in a 100 Å water box. 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. The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). 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]). CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. The obtained structures represent the lowest energy frame of the MD simulations. The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).\n\nProtein-protein docking\nCrystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. 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]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T26","span":{"begin":1152,"end":1153},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T27","span":{"begin":1158,"end":1159},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T28","span":{"begin":1393,"end":1395},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T29","span":{"begin":1464,"end":1466},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T30","span":{"begin":1620,"end":1625},"obj":"http://purl.obolibrary.org/obo/UBERON_0007688"},{"id":"T31","span":{"begin":1758,"end":1760},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T32","span":{"begin":2377,"end":2378},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T33","span":{"begin":2501,"end":2503},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"}],"text":"Materials and Methods\n\nSequence analysis\nSequences analyzed were individually retrieved from GenBank (accession numbers are shown in the phylogenetic tree, see Figure 1(Fig. 1)). 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).\n\nProtein modeling\nHomology 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]). Several models were obtained and the quality of each structure was evaluated. The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. These models were subjected to further protein structure optimization. Hydrogen atoms were added and the partial charges were assigned for energy refinement. The protein model was embedded in a 100 Å water box. 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. The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). 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]). CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. The obtained structures represent the lowest energy frame of the MD simulations. The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).\n\nProtein-protein docking\nCrystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. 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]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

LitCovid-PD-CHEBI

LitCovid-sentences

MyTest

{"project":"MyTest","denotations":[{"id":"32210742-16301204-29811227","span":{"begin":642,"end":643},"obj":"16301204"},{"id":"32210742-31762727-29811228","span":{"begin":1455,"end":1456},"obj":"31762727"},{"id":"32210742-16222654-29811229","span":{"begin":1556,"end":1558},"obj":"16222654"},{"id":"32210742-15368917-29811230","span":{"begin":1602,"end":1603},"obj":"15368917"},{"id":"32210742-19575467-29811231","span":{"begin":1655,"end":1657},"obj":"19575467"},{"id":"32210742-17517781-29811232","span":{"begin":1856,"end":1858},"obj":"17517781"},{"id":"32210742-24532726-29811233","span":{"begin":2501,"end":2503},"obj":"24532726"},{"id":"32210742-27503228-29811234","span":{"begin":2625,"end":2627},"obj":"27503228"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"Materials and Methods\n\nSequence analysis\nSequences analyzed were individually retrieved from GenBank (accession numbers are shown in the phylogenetic tree, see Figure 1(Fig. 1)). 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).\n\nProtein modeling\nHomology 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]). Several models were obtained and the quality of each structure was evaluated. The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. These models were subjected to further protein structure optimization. Hydrogen atoms were added and the partial charges were assigned for energy refinement. The protein model was embedded in a 100 Å water box. 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. The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). 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]). CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. The obtained structures represent the lowest energy frame of the MD simulations. The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).\n\nProtein-protein docking\nCrystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. 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]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

2_test

{"project":"2_test","denotations":[{"id":"32210742-16301204-29811227","span":{"begin":642,"end":643},"obj":"16301204"},{"id":"32210742-31762727-29811228","span":{"begin":1455,"end":1456},"obj":"31762727"},{"id":"32210742-16222654-29811229","span":{"begin":1556,"end":1558},"obj":"16222654"},{"id":"32210742-15368917-29811230","span":{"begin":1602,"end":1603},"obj":"15368917"},{"id":"32210742-19575467-29811231","span":{"begin":1655,"end":1657},"obj":"19575467"},{"id":"32210742-17517781-29811232","span":{"begin":1856,"end":1858},"obj":"17517781"},{"id":"32210742-24532726-29811233","span":{"begin":2501,"end":2503},"obj":"24532726"},{"id":"32210742-27503228-29811234","span":{"begin":2625,"end":2627},"obj":"27503228"}],"text":"Materials and Methods\n\nSequence analysis\nSequences analyzed were individually retrieved from GenBank (accession numbers are shown in the phylogenetic tree, see Figure 1(Fig. 1)). 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).\n\nProtein modeling\nHomology 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]). Several models were obtained and the quality of each structure was evaluated. The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC). On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD. These models were subjected to further protein structure optimization. Hydrogen atoms were added and the partial charges were assigned for energy refinement. The protein model was embedded in a 100 Å water box. 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. The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]). 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]). CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used. The obtained structures represent the lowest energy frame of the MD simulations. The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).\n\nProtein-protein docking\nCrystal structure for SARS-CoV spike (PDB code 6ACK) and ACE2 (PDB code 1R42) were downloaded from the Protein Data Bank. Also, the homology model for SARS-CoV-2 spike was assayed. Protein preparation was carried out as described above. Then, binding patterns and affinity estimations for the interaction between the viral spike and ACE2 receptor were performed using molecular docking. 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]). Then, the resulting docking data were processed and analyzed by using the tools of PRODIGY software (Xue et al., 2016[19]). Finally, results were clustered and analyzed considering binding energies and main interacting residues in each complex."}

PMC:7081066 / 3224-5975 JSONTXT

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PMC:7081066 / 3224-5975 JSON TXT