PMC:7245302 / 15771-16823 JSONTXT

{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/7245302","sourcedb":"PMC","sourceid":"7245302","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7245302","text":"2.8 Estimation of Binding Free Energies\nIn order to estimate the MMPBSA binding free energies for the receptors and multi-epitope peptide vaccine construct, the MMPBSA.py module [56] of AMBER16 was castoff. The program generated the input files for the complex, receptor and MEPVC molecule using the ante-MMPBSA.py module. To compute the variance between the solvated and un-solvated phases, 100 frames of simulation trajectories were picked and analyzed [57]. For the precise values of binding free energies, the two different conformations were matched to the binding energies of significant residues. To estimate the free binding energy of the anticipated complex, ΔGbind, solv was resolved using the three equations (Eqn 1,Eqn 2,Eqn 3 ) given below:(1) ΔGbind,solv=ΔGbind,vaccum+ΔGsolv,complex−ΔGsolv,ligand−ΔGsolv,complex (2) ΔGsolv=ΔGelectrostatic(ϵ80−1)+ΔGhydrophobic (3) ΔGvaccum=ΔEmolecularmechanics−−T.ΔGnormalmodeanalysis\nThe net free binding energy was then decomposition into each residue to highlight the interacting and stable residues.","divisions":[{"label":"label","span":{"begin":0,"end":3}},{"label":"title","span":{"begin":5,"end":40}},{"label":"p","span":{"begin":41,"end":933}},{"label":"label","span":{"begin":754,"end":757}},{"label":"label","span":{"begin":828,"end":831}},{"label":"label","span":{"begin":876,"end":879}}],"tracks":[{"project":"LitCovid-PD-CLO","denotations":[{"id":"T132","span":{"begin":131,"end":138},"obj":"http://purl.obolibrary.org/obo/PR_000018263"}],"attributes":[{"subj":"T132","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T93","span":{"begin":123,"end":130},"obj":"Chemical"},{"id":"T94","span":{"begin":131,"end":138},"obj":"Chemical"},{"id":"T95","span":{"begin":282,"end":290},"obj":"Chemical"},{"id":"T96","span":{"begin":806,"end":812},"obj":"Chemical"}],"attributes":[{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_53000"},{"id":"A94","pred":"chebi_id","subj":"T94","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A95","pred":"chebi_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"id":"A96","pred":"chebi_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"subj":"T93","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T94","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T95","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T96","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T119","span":{"begin":0,"end":40},"obj":"Sentence"},{"id":"T120","span":{"begin":41,"end":207},"obj":"Sentence"},{"id":"T121","span":{"begin":208,"end":323},"obj":"Sentence"},{"id":"T122","span":{"begin":324,"end":461},"obj":"Sentence"},{"id":"T123","span":{"begin":462,"end":604},"obj":"Sentence"},{"id":"T124","span":{"begin":605,"end":933},"obj":"Sentence"},{"id":"T125","span":{"begin":934,"end":1052},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T119","pred":"source","obj":"LitCovid-sentences"},{"subj":"T120","pred":"source","obj":"LitCovid-sentences"},{"subj":"T121","pred":"source","obj":"LitCovid-sentences"},{"subj":"T122","pred":"source","obj":"LitCovid-sentences"},{"subj":"T123","pred":"source","obj":"LitCovid-sentences"},{"subj":"T124","pred":"source","obj":"LitCovid-sentences"},{"subj":"T125","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-CLO","color":"#ec93aa","default":true},{"id":"LitCovid-PD-CHEBI","color":"#93c4ec"},{"id":"LitCovid-sentences","color":"#deec93"}]}]}}