PMC:7443692 / 66045-67708 JSONTXT

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T443","span":{"begin":128,"end":133},"obj":"Chemical"},{"id":"T444","span":{"begin":227,"end":232},"obj":"Chemical"},{"id":"T445","span":{"begin":759,"end":771},"obj":"Chemical"},{"id":"T446","span":{"begin":776,"end":783},"obj":"Chemical"},{"id":"T447","span":{"begin":1190,"end":1198},"obj":"Chemical"},{"id":"T448","span":{"begin":1407,"end":1412},"obj":"Chemical"},{"id":"T449","span":{"begin":1474,"end":1479},"obj":"Chemical"},{"id":"T450","span":{"begin":1487,"end":1494},"obj":"Chemical"}],"attributes":[{"id":"A448","pred":"chebi_id","subj":"T448","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A445","pred":"chebi_id","subj":"T445","obj":"http://purl.obolibrary.org/obo/CHEBI_16646"},{"id":"A443","pred":"chebi_id","subj":"T443","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A446","pred":"chebi_id","subj":"T446","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A450","pred":"chebi_id","subj":"T450","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A444","pred":"chebi_id","subj":"T444","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A449","pred":"chebi_id","subj":"T449","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A447","pred":"chebi_id","subj":"T447","obj":"http://purl.obolibrary.org/obo/CHEBI_49637"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T438","span":{"begin":0,"end":199},"obj":"Sentence"},{"id":"T439","span":{"begin":200,"end":395},"obj":"Sentence"},{"id":"T440","span":{"begin":396,"end":638},"obj":"Sentence"},{"id":"T441","span":{"begin":639,"end":807},"obj":"Sentence"},{"id":"T442","span":{"begin":808,"end":1001},"obj":"Sentence"},{"id":"T443","span":{"begin":1002,"end":1054},"obj":"Sentence"},{"id":"T444","span":{"begin":1055,"end":1164},"obj":"Sentence"},{"id":"T445","span":{"begin":1165,"end":1299},"obj":"Sentence"},{"id":"T446","span":{"begin":1300,"end":1413},"obj":"Sentence"},{"id":"T447","span":{"begin":1414,"end":1662},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T108","span":{"begin":1124,"end":1127},"obj":"Disease"}],"attributes":[{"id":"A108","pred":"mondo_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/MONDO_0020074"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T164","span":{"begin":1545,"end":1555},"obj":"http://purl.obolibrary.org/obo/IDO_0000607"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T220","span":{"begin":759,"end":771},"obj":"Body_part"},{"id":"T221","span":{"begin":776,"end":783},"obj":"Body_part"},{"id":"T222","span":{"begin":1487,"end":1494},"obj":"Body_part"}],"attributes":[{"id":"A220","pred":"fma_id","subj":"T220","obj":"http://purl.org/sig/ont/fma/fma82737"},{"id":"A221","pred":"fma_id","subj":"T221","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A222","pred":"fma_id","subj":"T222","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T133","span":{"begin":884,"end":894},"obj":"http://purl.obolibrary.org/obo/GO_0065007"},{"id":"T134","span":{"begin":990,"end":1000},"obj":"http://purl.obolibrary.org/obo/GO_0065007"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T126","span":{"begin":884,"end":894},"obj":"http://purl.obolibrary.org/obo/GO_0065007"},{"id":"T127","span":{"begin":990,"end":1000},"obj":"http://purl.obolibrary.org/obo/GO_0065007"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"LitCovid-sample-Glycan","denotations":[{"id":"T2947","span":{"begin":396,"end":399},"obj":"https://glytoucan.org/Structures/Glycans/G05518TD"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}

{"project":"2_test","denotations":[{"id":"32841605-22582031-19659569","span":{"begin":507,"end":511},"obj":"22582031"},{"id":"32841605-26592383-19659570","span":{"begin":536,"end":540},"obj":"26592383"},{"id":"32841605-17849372-19659571","span":{"begin":684,"end":688},"obj":"17849372"},{"id":"32841605-26574453-19659572","span":{"begin":731,"end":735},"obj":"26574453"},{"id":"32841605-8119250-19659573","span":{"begin":1158,"end":1162},"obj":"8119250"}],"text":"Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge. Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions. All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego). The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively. A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation. A nonbonded interaction cut-off of 8 Å was employed. Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993). Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed. The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms. Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.\n"}