{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T15:43:26Z","timestamp":1764603806079,"version":"3.37.3"},"reference-count":29,"publisher":"American Chemical Society (ACS)","issue":"11","license":[{"start":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-001"},{"start":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-009"},{"start":{"date-parts":[[2021,11,4]],"date-time":"2021-11-04T00:00:00Z","timestamp":1635984000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda????o para a Ci??ncia e a Tecnologia","doi-asserted-by":"publisher","award":["CEECIND\/02300\/2017","DSAIPA\/DS\/0118\/2020","LA\/P\/0058\/2020","PD\/BD\/135179\/2017","POCI-01-0145-FEDER-031356","PTDC\/BIA-BFS\/28419\/2017","PTDC\/QUI-OUT\/32243\/2017","SFRH\/BD\/140886\/2018","SFRH\/BD\/145457\/2019","UIDB\/04539\/2020","UIDP\/04539\/2020"],"award-info":[{"award-number":["CEECIND\/02300\/2017","DSAIPA\/DS\/0118\/2020","LA\/P\/0058\/2020","PD\/BD\/135179\/2017","POCI-01-0145-FEDER-031356","PTDC\/BIA-BFS\/28419\/2017","PTDC\/QUI-OUT\/32243\/2017","SFRH\/BD\/140886\/2018","SFRH\/BD\/145457\/2019","UIDB\/04539\/2020","UIDP\/04539\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["ACS Synth. Biol."],"published-print":{"date-parts":[[2021,11,19]]},"DOI":"10.1021\/acssynbio.1c00368","type":"journal-article","created":{"date-parts":[[2021,11,5]],"date-time":"2021-11-05T00:08:37Z","timestamp":1636070917000},"page":"3209-3235","source":"Crossref","is-referenced-by-count":13,"title":["In Silico End-to-End Protein\u2013Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2"],"prefix":"10.1021","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7225-9287","authenticated-orcid":true,"given":"N\u00edcia","family":"Ros\u00e1rio-Ferreira","sequence":"first","affiliation":[{"name":"Coimbra Chemistry Center, Chemistry Department, Faculty of Science and Technology, University of Coimbra, Coimbra 3004-535, Portugal"},{"name":"CNC\u2500Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, Cantanhede 3060-197, Portugal"}]},{"given":"Salete J.","family":"Baptista","sequence":"additional","affiliation":[{"name":"CNC\u2500Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, Cantanhede 3060-197, Portugal"},{"name":"Centro de Ci\u00eancias e Tecnologias Nucleares, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Estrada Nacional 10, ao km 139,7, Bobadela 2695-066, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1459-7680","authenticated-orcid":true,"given":"Carlos A. V.","family":"Barreto","sequence":"additional","affiliation":[{"name":"CNC\u2500Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, Cantanhede 3060-197, Portugal"},{"name":"PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra 3000-456, Portugal"}]},{"given":"Filipe E. P.","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"BioISI\u2500Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4608-2673","authenticated-orcid":true,"given":"Tom\u00e1s F. D.","family":"Silva","sequence":"additional","affiliation":[{"name":"BioISI\u2500Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal"}]},{"given":"Sara G. F.","family":"Ferreira","sequence":"additional","affiliation":[{"name":"BioISI\u2500Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal"}]},{"given":"Jo\u00e3o N. M.","family":"Vitorino","sequence":"additional","affiliation":[{"name":"BioISI\u2500Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1056-1007","authenticated-orcid":true,"given":"Rita","family":"Melo","sequence":"additional","affiliation":[{"name":"CNC\u2500Center for Neuroscience and Cell Biology. University of Coimbra, UC Biotech Building, Cantanhede 3060-197, Portugal"},{"name":"Centro de Ci\u00eancias e Tecnologias Nucleares, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Estrada Nacional 10, ao km 139,7, Bobadela 2695-066, Portugal"}]},{"given":"Bruno L.","family":"Victor","sequence":"additional","affiliation":[{"name":"BioISI\u2500Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6923-8744","authenticated-orcid":true,"given":"Miguel","family":"Machuqueiro","sequence":"additional","affiliation":[{"name":"BioISI\u2500Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2970-5250","authenticated-orcid":true,"given":"Irina S.","family":"Moreira","sequence":"additional","affiliation":[{"name":"University of Coimbra, Center for Neurosciences and Cell Biology, Department of Life Sciences, Coimbra 3000-456, Portugal"}]}],"member":"316","published-online":{"date-parts":[[2021,11,4]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules25143193"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2020.107325"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb3405"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21103626"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2020.12.005"},{"key":"ref6\/cit6","unstructured":"The PyMOL Molecular\nGraphics System, ver. 2.4; Schr\u00f6dinger,\nLLC, 2020. https:\/\/pymol.org\/2\/."},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.3"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp259"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm290"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-2-5"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2015.09.014"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1002\/prot.25838"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.8b01226"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.5772\/intechopen.85991"},{"key":"ref15\/cit15","doi-asserted-by":"crossref","unstructured":"Zhang, W; Hu, Z. Faculty Opinions recommendation of Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved \u03b1-ketoamide inhibitors.  Faculty Opinions, 2020. https:\/\/facultyopinions.com\/prime\/737592020.","DOI":"10.3410\/f.737592020.793572879"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0017695"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21197281"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1002\/prot.24078"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.3389\/fchem.2020.00343"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21334"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2016.051"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1039\/C9CP06303J"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-3-33"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1021\/ci500588j"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1016\/j.softx.2015.06.001"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2020.1794974"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2018.08.011"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1186\/2046-1682-5-9"}],"container-title":["ACS Synthetic Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acssynbio.1c00368","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T03:10:41Z","timestamp":1682651441000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acssynbio.1c00368"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,4]]},"references-count":29,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2021,11,19]]}},"alternative-id":["10.1021\/acssynbio.1c00368"],"URL":"https:\/\/doi.org\/10.1021\/acssynbio.1c00368","relation":{},"ISSN":["2161-5063","2161-5063"],"issn-type":[{"type":"print","value":"2161-5063"},{"type":"electronic","value":"2161-5063"}],"subject":[],"published":{"date-parts":[[2021,11,4]]}}}