{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T06:35:18Z","timestamp":1773815718825,"version":"3.50.1"},"reference-count":20,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2022,8,27]],"date-time":"2022-08-27T00:00:00Z","timestamp":1661558400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FCT","award":["UIDP\/04378\/2020"],"award-info":[{"award-number":["UIDP\/04378\/2020"]}]},{"name":"FCT","award":["UIDB\/04378\/2020"],"award-info":[{"award-number":["UIDB\/04378\/2020"]}]},{"name":"FCT","award":["2020.01423.CEECIND"],"award-info":[{"award-number":["2020.01423.CEECIND"]}]},{"name":"FCT","award":["01\/SAICT\/2016 022153"],"award-info":[{"award-number":["01\/SAICT\/2016 022153"]}]},{"name":"FCT","award":["CPCA\/A1\/422043\/2021"],"award-info":[{"award-number":["CPCA\/A1\/422043\/2021"]}]},{"name":"FCT","award":["PTDC\/QUI-QFI\/31689\/2017"],"award-info":[{"award-number":["PTDC\/QUI-QFI\/31689\/2017"]}]},{"name":"FCT","award":["UIDP\/04378\/2020"],"award-info":[{"award-number":["UIDP\/04378\/2020"]}]},{"name":"FCT","award":["UIDB\/04378\/2020"],"award-info":[{"award-number":["UIDB\/04378\/2020"]}]},{"name":"FCT","award":["2020.01423.CEECIND"],"award-info":[{"award-number":["2020.01423.CEECIND"]}]},{"name":"FCT","award":["01\/SAICT\/2016 022153"],"award-info":[{"award-number":["01\/SAICT\/2016 022153"]}]},{"name":"FCT","award":["CPCA\/A1\/422043\/2021"],"award-info":[{"award-number":["CPCA\/A1\/422043\/2021"]}]},{"name":"FCT","award":["PTDC\/QUI-QFI\/31689\/2017"],"award-info":[{"award-number":["PTDC\/QUI-QFI\/31689\/2017"]}]},{"name":"FCT","award":["UIDP\/04378\/2020"],"award-info":[{"award-number":["UIDP\/04378\/2020"]}]},{"name":"FCT","award":["UIDB\/04378\/2020"],"award-info":[{"award-number":["UIDB\/04378\/2020"]}]},{"name":"FCT","award":["2020.01423.CEECIND"],"award-info":[{"award-number":["2020.01423.CEECIND"]}]},{"name":"FCT","award":["01\/SAICT\/2016 022153"],"award-info":[{"award-number":["01\/SAICT\/2016 022153"]}]},{"name":"FCT","award":["CPCA\/A1\/422043\/2021"],"award-info":[{"award-number":["CPCA\/A1\/422043\/2021"]}]},{"name":"FCT","award":["PTDC\/QUI-QFI\/31689\/2017"],"award-info":[{"award-number":["PTDC\/QUI-QFI\/31689\/2017"]}]},{"name":"FCT","award":["UIDP\/04378\/2020"],"award-info":[{"award-number":["UIDP\/04378\/2020"]}]},{"name":"FCT","award":["UIDB\/04378\/2020"],"award-info":[{"award-number":["UIDB\/04378\/2020"]}]},{"name":"FCT","award":["2020.01423.CEECIND"],"award-info":[{"award-number":["2020.01423.CEECIND"]}]},{"name":"FCT","award":["01\/SAICT\/2016 022153"],"award-info":[{"award-number":["01\/SAICT\/2016 022153"]}]},{"name":"FCT","award":["CPCA\/A1\/422043\/2021"],"award-info":[{"award-number":["CPCA\/A1\/422043\/2021"]}]},{"name":"FCT","award":["PTDC\/QUI-QFI\/31689\/2017"],"award-info":[{"award-number":["PTDC\/QUI-QFI\/31689\/2017"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand\u2013protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics\/molecular mechanics (QM\/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store.<\/jats:p>","DOI":"10.3390\/molecules27175524","type":"journal-article","created":{"date-parts":[[2022,8,29]],"date-time":"2022-08-29T22:53:42Z","timestamp":1661813622000},"page":"5524","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9280-1838","authenticated-orcid":false,"given":"Henrique S.","family":"Fernandes","sequence":"first","affiliation":[{"name":"Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal"},{"name":"UCIBIO\u2013Applied Molecular Biosciences Unit, BioSIM\u2014Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal"}]},{"given":"Nuno M. F. S. A.","family":"Cerqueira","sequence":"additional","affiliation":[{"name":"Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal"},{"name":"UCIBIO\u2013Applied Molecular Biosciences Unit, BioSIM\u2014Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6560-5284","authenticated-orcid":false,"given":"S\u00e9rgio F.","family":"Sousa","sequence":"additional","affiliation":[{"name":"Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal"},{"name":"UCIBIO\u2013Applied Molecular Biosciences Unit, BioSIM\u2014Departamento de Biomedicina, Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal"}]},{"given":"Andr\u00e9","family":"Melo","sequence":"additional","affiliation":[{"name":"Faculdade de Ci\u00eancias, Universidade do Porto, Rua do Campo Alegre 1021 1055, 4169-007 Porto, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,27]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3281","DOI":"10.2174\/13816128113199990600","article-title":"Molecular Mechanics","volume":"20","author":"Vanommeslaeghe","year":"2014","journal-title":"Curr. Pharm. Des."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1373","DOI":"10.1007\/s11030-021-10259-7","article-title":"New Insights into the Catalytic Mechanism of the SARS-CoV-2 Main Protease: An ONIOM QM\/MM Approach","volume":"26","author":"Fernandes","year":"2021","journal-title":"Mol. Divers"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1039\/D0SC06195F","article-title":"Mechanism of Inhibition of SARS-CoV-2 M pro by N3 Peptidyl Michael Acceptor Explained by QM\/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity","volume":"12","author":"Arafet","year":"2021","journal-title":"Chem. 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[Master\u2019s Thesis, Faculdade de Ci\u00eancias da Universidade do Porto em Bioqu\t\u00edmica]."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"3041","DOI":"10.1021\/acs.jcim.1c00394","article-title":"QM\/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate","volume":"61","author":"Boneta","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e202100555","DOI":"10.1002\/cbic.202100555","article-title":"The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study","volume":"23","author":"Pina","year":"2021","journal-title":"ChemBioChem"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Magalh\u00e3es, R., Vieira, T., Fernandes, H., Cerqueira, N., Melo, A., Sim\u00f5es, M., and Sousa, S. (2018, January 19). Creation of a Structural Database for Inhibition of Biofilm Formation. 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