PMC:7544943 / 15032-16539 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T16","span":{"begin":599,"end":607},"obj":"Body_part"},{"id":"T17","span":{"begin":633,"end":641},"obj":"Body_part"},{"id":"T18","span":{"begin":707,"end":714},"obj":"Body_part"},{"id":"T19","span":{"begin":856,"end":863},"obj":"Body_part"}],"attributes":[{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma61788"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma61788"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"2.5. Mm/PBSA binding free energy calculation\nThe method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T44","span":{"begin":818,"end":820},"obj":"Disease"},{"id":"T46","span":{"begin":879,"end":881},"obj":"Disease"}],"attributes":[{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0010979"},{"id":"A45","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0016455"},{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0010979"},{"id":"A47","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0016455"}],"text":"2.5. Mm/PBSA binding free energy calculation\nThe method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T69","span":{"begin":100,"end":102},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T70","span":{"begin":312,"end":314},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T71","span":{"begin":937,"end":938},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T72","span":{"begin":1227,"end":1228},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"2.5. Mm/PBSA binding free energy calculation\nThe method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively."}

{"project":"LitCovid-PubTator","denotations":[{"id":"277","span":{"begin":9,"end":13},"obj":"Chemical"},{"id":"279","span":{"begin":957,"end":958},"obj":"Chemical"}],"attributes":[{"id":"A277","pred":"tao:has_database_id","subj":"277","obj":"MESH:C437084"},{"id":"A279","pred":"tao:has_database_id","subj":"279","obj":"MESH:D013455"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"2.5. Mm/PBSA binding free energy calculation\nThe method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively."}

{"project":"LitCovid-sentences","denotations":[{"id":"T142","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T143","span":{"begin":6,"end":45},"obj":"Sentence"},{"id":"T144","span":{"begin":46,"end":207},"obj":"Sentence"},{"id":"T145","span":{"begin":208,"end":399},"obj":"Sentence"},{"id":"T146","span":{"begin":400,"end":531},"obj":"Sentence"},{"id":"T147","span":{"begin":532,"end":749},"obj":"Sentence"},{"id":"T148","span":{"begin":750,"end":986},"obj":"Sentence"},{"id":"T149","span":{"begin":987,"end":1340},"obj":"Sentence"},{"id":"T150","span":{"begin":1341,"end":1507},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.5. Mm/PBSA binding free energy calculation\nThe method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively."}

{"project":"2_test","denotations":[{"id":"32938313-11517324-56197384","span":{"begin":372,"end":376},"obj":"11517324"},{"id":"32938313-24850022-56197385","span":{"begin":393,"end":397},"obj":"24850022"}],"text":"2.5. Mm/PBSA binding free energy calculation\nThe method of calculation of binding free energy from MD trajectory snapshots using the molecular mechanics Poisson–Boltzmann surface area method is widely used. The binding free energy of the systems was estimated by extracting the snaps from the last 20 ns of the MD simulation using g_mmpbsa tool of Gromacs (Baker et al., 2001; Kumari et al., 2014). The binding free energy takes the contribution from vacuum potential energy, polar solvation energy and non-polar solvation energy. The binding free energy can be represented as (1) ΔGbind=Gcomplex−(Gprotein+Gligand) where Gcomplex, Gprotein and Gligand are the total free energies of the complex, isolated protein and isolated ligand, respectively. The free energy of the individual terms was estimated by (2) Gx=EMM−TS+Gsolvation where x is the complex, protein or ligand, and TS represents the entropic contribution to free energy in a vacuum with T and S as temperature and entropy. The average molecular mechanics potential and solvation free energies were calculated by using Equations (3) and (4) (3) EMM=Ebonded+Enonbonded= Ebonded−(Eelec+Evdw) (4) Gsolvation=Gpolar+Gnonpolar where Ebonded takes the contribution from a bond, angle and dihedral terms and Enonbonded consists of electrostatic and van der Waals energy contributions. The solvation energy includes the polar and non-polar solvation energies from the Poisson–Boltzmann equation and solvent accessible surface area (SASA), respectively."}