{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T13:15:09Z","timestamp":1769951709459,"version":"3.49.0"},"reference-count":65,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2023,8,2]],"date-time":"2023-08-02T00:00:00Z","timestamp":1690934400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2023,8,2]],"date-time":"2023-08-02T00:00:00Z","timestamp":1690934400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mol Divers"],"published-print":{"date-parts":[[2024,10]]},"DOI":"10.1007\/s11030-023-10705-8","type":"journal-article","created":{"date-parts":[[2023,8,2]],"date-time":"2023-08-02T12:01:33Z","timestamp":1690977693000},"page":"2735-2748","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Cheminformatics and machine learning approaches for repurposing anti-viral compounds against monkeypox virus thymidylate kinase"],"prefix":"10.1007","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6774-9847","authenticated-orcid":false,"given":"Ali A.","family":"Rabaan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ameen S. S.","family":"Alwashmi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mutaib M.","family":"Mashraqi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmad A.","family":"Alshehri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdulsalam","family":"Alawfi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amer","family":"Alshengeti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mustafa A.","family":"Najim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bashayer M.","family":"AlShehail","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdullah J.","family":"AlShahrani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1317-1186","authenticated-orcid":false,"given":"Mohammed","family":"Garout","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,8,2]]},"reference":[{"key":"10705_CR1","unstructured":"Kimball S CDC says monkeypox doesn\u2019t spread easily by air: \u2018This is not Covid\u2019. CNBC. Accessed 15 Nov 2022. https:\/\/www.cnbc.com\/2022\/05\/24\/cdc-says-monkeypox-doesnt-spread-easily-by-air-this-is-not-covid.html"},{"key":"10705_CR2","doi-asserted-by":"publisher","first-page":"D54","DOI":"10.1016\/j.vaccine.2011.04.014","volume":"29","author":"IK Damon","year":"2011","unstructured":"Damon IK (2011) Status of human monkeypox: clinical disease, epidemiology and research. Vaccine 29:D54\u2013D59. https:\/\/doi.org\/10.1016\/j.vaccine.2011.04.014","journal-title":"Vaccine"},{"issue":"5","key":"10705_CR3","first-page":"599","volume":"46","author":"SS Marennikova","year":"1972","unstructured":"Marennikova SS, Seluhina EM, SeluhinaMal\u2019ceva NN, Cimiskjan KL, Macevic GR EM (1972) Isolation and properties of the causal agent of a new variola-like disease (monkeypox) in man. Bull World Health Organ 46(5):599\u2013611","journal-title":"Bull World Health Organ"},{"issue":"5","key":"10705_CR4","first-page":"593","volume":"46","author":"ID Ladnyj","year":"1972","unstructured":"Ladnyj ID, Ziegler P, Kima E (1972) A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo. Bull World Health Organ 46(5):593\u2013597","journal-title":"Bull World Health Organ"},{"key":"10705_CR5","unstructured":"Human Monkeypox\u2014Kasai Oriental, Zaire, 1996\u20131997. Accessed 9 Sept 2022. https:\/\/www.cdc.gov\/mmwr\/preview\/mmwrhtml\/00048673.htm"},{"issue":"10","key":"10705_CR6","doi-asserted-by":"publisher","first-page":"306","DOI":"10.15585\/mmwr.mm6710a5","volume":"67","author":"KN Durski","year":"2018","unstructured":"Durski KN, McCollum AM, Nakazawa Y et al (2018) Emergence of monkeypox\u2014West and Central Africa, 1970\u20132017. MMWR Morb Mortal Wkly Rep 67(10):306\u2013310. https:\/\/doi.org\/10.15585\/mmwr.mm6710a5","journal-title":"MMWR Morb Mortal Wkly Rep"},{"issue":"2","key":"10705_CR7","doi-asserted-by":"publisher","first-page":"e0010141","DOI":"10.1371\/journal.pntd.0010141","volume":"16","author":"EM Bunge","year":"2022","unstructured":"Bunge EM, Hoet B, Chen L et al (2022) The changing epidemiology of human monkeypox\u2014a potential threat? A systematic review. Gromowski G, ed. PLoS Negl Trop Dis 16(2):e0010141. https:\/\/doi.org\/10.1371\/journal.pntd.0010141","journal-title":"PLoS Negl Trop Dis"},{"issue":"6","key":"10705_CR8","doi-asserted-by":"publisher","first-page":"773","DOI":"10.1086\/505880","volume":"194","author":"MG Reynolds","year":"2006","unstructured":"Reynolds MG, Yorita KL, Kuehnert MJ et al (2006) Clinical manifestations of human Monkeypox influenced by route of infection. J Infect Dis 194(6):773\u2013780. https:\/\/doi.org\/10.1086\/505880","journal-title":"J Infect Dis"},{"key":"10705_CR9","unstructured":"Multi-country monkeypox outbreak: situation update. Accessed 5 Sept 2022. https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2022-DON390"},{"key":"10705_CR10","unstructured":"Monkeypox: background information. GOV.UK. Accessed 5 Sept 2022. https:\/\/www.gov.uk\/guidance\/monkeypox"},{"issue":"4","key":"10705_CR11","first-page":"465","volume":"66","author":"Z Jezek","year":"1988","unstructured":"Jezek Z, Grab B, Szczeniowski MV, Paluku KM, Mutombo M (1988) Human monkeypox: secondary attack rates. Bull World Health Organ 66(4):465\u2013470","journal-title":"Bull World Health Organ"},{"issue":"2","key":"10705_CR12","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1099\/vir.0.005108-0","volume":"90","author":"CL Hutson","year":"2009","unstructured":"Hutson CL, Olson VA, Carroll DS et al (2009) A prairie dog animal model of systemic orthopoxvirus disease using West African and Congo Basin strains of monkeypox virus. J Gen Virol 90(2):323\u2013333. https:\/\/doi.org\/10.1099\/vir.0.005108-0","journal-title":"J Gen Virol"},{"issue":"3","key":"10705_CR13","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1093\/oxfordjournals.bmb.a011720","volume":"54","author":"DL Heymann","year":"1998","unstructured":"Heymann DL, Szczeniowski M, Esteves K (1998) Re-emergence of monkeypox in Africa: a review of the past six years. Br Med Bull 54(3):693\u2013702. https:\/\/doi.org\/10.1093\/oxfordjournals.bmb.a011720","journal-title":"Br Med Bull"},{"issue":"11","key":"10705_CR14","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.3390\/v12111257","volume":"12","author":"E Alakunle","year":"2020","unstructured":"Alakunle E, Moens U, Nchinda G, Okeke MI (2020) Monkeypox virus in Nigeria: infection biology, epidemiology, and evolution. Viruses 12(11):1257. https:\/\/doi.org\/10.3390\/v12111257","journal-title":"Viruses"},{"key":"10705_CR15","volume-title":"Mandell, Douglas, and Bennett\u2019s principles and practice of infectious diseases","author":"JE Bennett","year":"2019","unstructured":"Bennett JE, Dolin R, Blaser MJ (2019) Mandell, Douglas, and Bennett\u2019s principles and practice of infectious diseases. Elsevier, Amsterdam"},{"issue":"4","key":"10705_CR16","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1016\/j.idc.2019.03.001","volume":"33","author":"E Petersen","year":"2019","unstructured":"Petersen E, Kantele A, Koopmans M et al (2019) Human monkeypox: epidemiologic and clinical characteristics, diagnosis, and prevention. Infect Dis Clin 33(4):1027\u20131043. https:\/\/doi.org\/10.1016\/j.idc.2019.03.001","journal-title":"Infect Dis Clin"},{"issue":"1","key":"10705_CR17","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.virol.2005.05.030","volume":"340","author":"N Chen","year":"2005","unstructured":"Chen N, Li G, Liszewski MK et al (2005) Virulence differences between monkeypox virus isolates from West Africa and the Congo basin. Virology 340(1):46\u201363. https:\/\/doi.org\/10.1016\/j.virol.2005.05.030","journal-title":"Virology"},{"issue":"8","key":"10705_CR18","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1038\/s41591-022-01907-y","volume":"28","author":"J Isidro","year":"2022","unstructured":"Isidro J, Borges V, Pinto M et al (2022) Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nat Med 28(8):1569\u20131572. https:\/\/doi.org\/10.1038\/s41591-022-01907-y","journal-title":"Nat Med"},{"issue":"2","key":"10705_CR19","doi-asserted-by":"publisher","first-page":"232","DOI":"10.3201\/eid2002.130118","volume":"20","author":"JR Kugelman","year":"2014","unstructured":"Kugelman JR, Johnston SC, Mulembakani PM et al (2014) Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo. Emerg Infect Dis 20(2):232\u2013239. https:\/\/doi.org\/10.3201\/eid2002.130118","journal-title":"Emerg Infect Dis"},{"issue":"1","key":"10705_CR20","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/S0014-5793(01)03144-1","volume":"509","author":"SN Shchelkunov","year":"2001","unstructured":"Shchelkunov SN, Totmenin AV, Babkin IV et al (2001) Human monkeypox and smallpox viruses: genomic comparison. FEBS Lett 509(1):66\u201370. https:\/\/doi.org\/10.1016\/S0014-5793(01)03144-1","journal-title":"FEBS Lett"},{"key":"10705_CR21","doi-asserted-by":"publisher","DOI":"10.15212\/AMM-2022-0017","author":"L Zheng","year":"2022","unstructured":"Zheng L, Meng J, Lin M et al (2022) Structure prediction of the entire proteome of monkeypox variants. Acta Materia Medica. https:\/\/doi.org\/10.15212\/AMM-2022-0017","journal-title":"Acta Materia Medica"},{"key":"10705_CR22","doi-asserted-by":"publisher","DOI":"10.1101\/2022.06.01.494368","author":"FM Giorgi","year":"2022","unstructured":"Giorgi FM, Pozzobon D, Di Meglio A, Mercatelli D (2022) Genomic analysis of the recent monkeypox outbreak. Bioinformatics. https:\/\/doi.org\/10.1101\/2022.06.01.494368","journal-title":"Bioinformatics"},{"key":"10705_CR23","doi-asserted-by":"publisher","DOI":"10.1101\/2022.08.07.503103","author":"G Minasov","year":"2022","unstructured":"Minasov G, Inniss NL, Shuvalova L, Anderson WF, Satchell KJF (2022) Structure of the monkeypox profilin-like protein A42R reveals potential function differences from cellular profilins. Microbiology. https:\/\/doi.org\/10.1101\/2022.08.07.503103","journal-title":"Microbiology"},{"key":"10705_CR24","volume-title":"Smallpox and its eradication","year":"1988","unstructured":"Fenner F (ed) (1988) Smallpox and its eradication. World Health Organization, Geneva"},{"issue":"3","key":"10705_CR25","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1093\/ije\/17.3.643","volume":"17","author":"PEM Fine","year":"1988","unstructured":"Fine PEM, Jezek Z, Grab B, Dixon H (1988) The transmission potential of monkeypox virus in human populations. Int J Epidemiol 17(3):643\u2013650. https:\/\/doi.org\/10.1093\/ije\/17.3.643","journal-title":"Int J Epidemiol"},{"issue":"1\u20132","key":"10705_CR26","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S0166-3542(02)00196-1","volume":"57","author":"RO Baker","year":"2003","unstructured":"Baker RO, Bray M, Huggins JW (2003) Potential antiviral therapeutics for smallpox, monkeypox and other orthopoxvirus infections. Antiviral Res 57(1\u20132):13\u201323. https:\/\/doi.org\/10.1016\/S0166-3542(02)00196-1","journal-title":"Antiviral Res"},{"key":"10705_CR27","unstructured":"Commissioner O of the FDA Provides Update on Agency Response to Monkeypox Outbreak FDA (2022) Accessed 5 Sept 2022. https:\/\/www.fda.gov\/news-events\/press-announcements\/fda-provides-update-agency-response-monkeypox-outbreak"},{"key":"10705_CR28","unstructured":"Drugs with antiviral activity against monkeypox virus\u2014MedMDS. https:\/\/www.medmds.com\/. Accessed 6 Sept 2022. https:\/\/www.medmds.com\/2022\/08\/02\/drugs-with-antiviral-activity-against-monkeypox-virus\/"},{"issue":"4","key":"10705_CR29","doi-asserted-by":"publisher","first-page":"e0149521","DOI":"10.1128\/mBio.01495-21","volume":"12","author":"TG Senkevich","year":"2021","unstructured":"Senkevich TG, Yutin N, Wolf YI, Koonin EV, Moss B (2021) Ancient gene capture and recent gene loss shape the evolution of orthopoxvirus-host interaction genes. MBio 12(4):e0149521. https:\/\/doi.org\/10.1128\/mBio.01495-21","journal-title":"MBio"},{"issue":"1","key":"10705_CR30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.virol.2008.11.045","volume":"385","author":"A MacNeil","year":"2009","unstructured":"MacNeil A, Reynolds MG, Damon IK (2009) Risks associated with vaccinia virus in the laboratory. Virology 385(1):1\u20134. https:\/\/doi.org\/10.1016\/j.virol.2008.11.045","journal-title":"Virology"},{"issue":"1","key":"10705_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.antiviral.2009.06.006","volume":"84","author":"BL Jacobs","year":"2009","unstructured":"Jacobs BL, Langland JO, Kibler KV et al (2009) Vaccinia virus vaccines: past, present and future. Antiviral Res 84(1):1\u201313. https:\/\/doi.org\/10.1016\/j.antiviral.2009.06.006","journal-title":"Antiviral Res"},{"issue":"2","key":"10705_CR32","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1006\/viro.1994.1288","volume":"201","author":"RF Massung","year":"1994","unstructured":"Massung RF, Liu LI, Qi J et al (1994) Analysis of the complete genome of smallpox variola major virus strain Bangladesh-1975. Virology 201(2):215\u2013240. https:\/\/doi.org\/10.1006\/viro.1994.1288","journal-title":"Virology"},{"issue":"11","key":"10705_CR33","doi-asserted-by":"publisher","first-page":"e01570","DOI":"10.1128\/genomeA.01570-17","volume":"6","author":"I Prazs\u00e1k","year":"2018","unstructured":"Prazs\u00e1k I, Tomb\u00e1cz D, Sz\u0171cs A, D\u00e9nes B, Snyder M, Boldogk\u0151i Z (2018) Full genome sequence of the western reserve strain of vaccinia virus determined by third-generation sequencing. Genome Announc 6(11):e01570-e1617. https:\/\/doi.org\/10.1128\/genomeA.01570-17","journal-title":"Genome Announc"},{"issue":"2","key":"10705_CR34","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.antiviral.2012.02.012","volume":"94","author":"MN Prichard","year":"2012","unstructured":"Prichard MN, Kern ER (2012) Orthopoxvirus targets for the development of new antiviral agents. Antivir Res 94(2):111\u2013125. https:\/\/doi.org\/10.1016\/j.antiviral.2012.02.012","journal-title":"Antivir Res"},{"issue":"44","key":"10705_CR35","doi-asserted-by":"publisher","first-page":"16900","DOI":"10.1073\/pnas.0804525105","volume":"105","author":"C Caillat","year":"2008","unstructured":"Caillat C, Topalis D, Agrofoglio LA et al (2008) Crystal structure of poxvirus thymidylate kinase: an unexpected dimerization has implications for antiviral therapy. Proc Natl Acad Sci 105(44):16900\u201316905. https:\/\/doi.org\/10.1073\/pnas.0804525105","journal-title":"Proc Natl Acad Sci"},{"issue":"12","key":"10705_CR36","doi-asserted-by":"publisher","first-page":"e3001464","DOI":"10.1371\/journal.pbio.3001464","volume":"19","author":"Y Wang","year":"2021","unstructured":"Wang Y, Wang Q, Huang H et al (2021) A crowdsourcing open platform for literature curation in UniProt. PLOS Biol 19(12):e3001464. https:\/\/doi.org\/10.1371\/journal.pbio.3001464","journal-title":"PLOS Biol"},{"issue":"7873","key":"10705_CR37","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper J, Evans R, Pritzel A et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596(7873):583\u2013589. https:\/\/doi.org\/10.1038\/s41586-021-03819-2","journal-title":"Nature"},{"issue":"3","key":"10705_CR38","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1023\/A:1011491422534","volume":"4","author":"G Allen","year":"2001","unstructured":"Allen G, Benger W, Dramlitsch T et al (2001) Cactus tools for grid applications. Clust Comput 4(3):179\u2013188. https:\/\/doi.org\/10.1023\/A:1011491422534","journal-title":"Clust Comput"},{"issue":"1","key":"10705_CR39","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1758-2946-3-33","volume":"3","author":"NM O\u2019Boyle","year":"2011","unstructured":"O\u2019Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 3(1):33. https:\/\/doi.org\/10.1186\/1758-2946-3-33","journal-title":"J Cheminform"},{"issue":"W1","key":"10705_CR40","doi-asserted-by":"publisher","first-page":"W363","DOI":"10.1093\/nar\/gky473","volume":"46","author":"W Tian","year":"2018","unstructured":"Tian W, Chen C, Lei X, Zhao J, Liang J (2018) CASTp 3.0: computed atlas of surface topography of proteins. Nucleic Acids Res 46(W1):W363\u2013W367. https:\/\/doi.org\/10.1093\/nar\/gky473","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"10705_CR41","doi-asserted-by":"publisher","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","volume":"61","author":"J Eberhardt","year":"2021","unstructured":"Eberhardt J, Santos-Martins D, Tillack AF, Forli S (2021) AutoDock Vina 1.2.0: new docking methods, expanded force field, and Python bindings. J Chem Inf Model 61(8):3891\u20133898. https:\/\/doi.org\/10.1021\/acs.jcim.1c00203","journal-title":"J Chem Inf Model"},{"issue":"5","key":"10705_CR42","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/nprot.2016.051","volume":"11","author":"S Forli","year":"2016","unstructured":"Forli S, Huey R, Pique ME, Sanner MF, Goodsell DS, Olson AJ (2016) Computational protein\u2013ligand docking and virtual drug screening with the AutoDock suite. Nat Protoc 11(5):905\u2013919. https:\/\/doi.org\/10.1038\/nprot.2016.051","journal-title":"Nat Protoc"},{"issue":"2","key":"10705_CR43","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2010","unstructured":"Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455\u2013461. https:\/\/doi.org\/10.1002\/jcc.21334","journal-title":"J Comput Chem"},{"issue":"16","key":"10705_CR44","doi-asserted-by":"publisher","first-page":"2785","DOI":"10.1002\/jcc.21256","volume":"30","author":"GM Morris","year":"2009","unstructured":"Morris GM, Huey R, Lindstrom W et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785\u20132791. https:\/\/doi.org\/10.1002\/jcc.21256","journal-title":"J Comput Chem"},{"key":"10705_CR45","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1016\/B978-0-12-821748-1.00015-4","volume-title":"Chemoinformatics and bioinformatics in the pharmaceutical sciences","author":"T Arora","year":"2021","unstructured":"Arora T, Malik AA (2021) An introduction to BLAST. Chemoinformatics and bioinformatics in the pharmaceutical sciences. Elsevier, Amseterdam, pp 423\u2013453"},{"issue":"W1","key":"10705_CR46","doi-asserted-by":"publisher","first-page":"W612","DOI":"10.1093\/nar\/gkv352","volume":"43","author":"M Davies","year":"2015","unstructured":"Davies M, Nowotka M, Papadatos G et al (2015) ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Res 43(W1):W612\u2013W620. https:\/\/doi.org\/10.1093\/nar\/gkv352","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"10705_CR47","doi-asserted-by":"publisher","first-page":"D1100","DOI":"10.1093\/nar\/gkr777","volume":"40","author":"A Gaulton","year":"2012","unstructured":"Gaulton A, Bellis LJ, Bento AP et al (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40(D1):D1100\u2013D1107. https:\/\/doi.org\/10.1093\/nar\/gkr777","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"10705_CR48","doi-asserted-by":"publisher","first-page":"D945","DOI":"10.1093\/nar\/gkw1074","volume":"45","author":"A Gaulton","year":"2017","unstructured":"Gaulton A, Hersey A, Nowotka M et al (2017) The ChEMBL database in 2017. Nucleic Acids Res 45(D1):D945\u2013D954. https:\/\/doi.org\/10.1093\/nar\/gkw1074","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"10705_CR49","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1002\/jcc.21707","volume":"32","author":"CW Yap","year":"2011","unstructured":"Yap CW (2011) PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J Comput Chem 32(7):1466\u20131474. https:\/\/doi.org\/10.1002\/jcc.21707","journal-title":"J Comput Chem"},{"issue":"1\u20133","key":"10705_CR50","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/0010-4655(95)00042-E","volume":"91","author":"HJC Berendsen","year":"1995","unstructured":"Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91(1\u20133):43\u201356. https:\/\/doi.org\/10.1016\/0010-4655(95)00042-E","journal-title":"Comput Phys Commun"},{"issue":"3","key":"10705_CR51","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435\u2013447. https:\/\/doi.org\/10.1021\/ct700301q","journal-title":"J Chem Theory Comput"},{"key":"10705_CR52","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R et al (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1:19\u201325. https:\/\/doi.org\/10.1016\/j.softx.2015.06.001","journal-title":"SoftwareX"},{"issue":"3","key":"10705_CR53","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435\u2013447. https:\/\/doi.org\/10.1021\/ct700301q","journal-title":"J Chem Theory Comput"},{"issue":"1","key":"10705_CR54","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1021\/acs.jctc.5b00935","volume":"12","author":"J Lee","year":"2016","unstructured":"Lee J, Cheng X, Swails JM et al (2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM\/OpenMM simulations using the CHARMM36 additive force field. J Chem Theory Comput 12(1):405\u2013413. https:\/\/doi.org\/10.1021\/acs.jctc.5b00935","journal-title":"J Chem Theory Comput"},{"issue":"12","key":"10705_CR55","doi-asserted-by":"publisher","first-page":"3155","DOI":"10.1021\/ci3003649","volume":"52","author":"K Vanommeslaeghe","year":"2012","unstructured":"Vanommeslaeghe K, Raman EP, MacKerell AD (2012) Automation of the CHARMM general force field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J Chem Inf Model 52(12):3155\u20133168. https:\/\/doi.org\/10.1021\/ci3003649","journal-title":"J Chem Inf Model"},{"issue":"12","key":"10705_CR56","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","volume":"98","author":"T Darden","year":"1993","unstructured":"Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N\u22c5log(N) method for Ewald sums in large systems. J Chem Phys 98(12):10089\u201310092. https:\/\/doi.org\/10.1063\/1.464397","journal-title":"J Chem Phys"},{"issue":"20","key":"10705_CR57","doi-asserted-by":"publisher","first-page":"10096","DOI":"10.1063\/1.1808117","volume":"121","author":"DJ Price","year":"2004","unstructured":"Price DJ, Brooks CL III (2004) A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys 121(20):10096\u201310103. https:\/\/doi.org\/10.1063\/1.1808117","journal-title":"J Chem Phys"},{"key":"10705_CR58","doi-asserted-by":"publisher","first-page":"e125071","DOI":"10.1155\/2012\/125071","volume":"2012","author":"Y Xu","year":"2012","unstructured":"Xu Y, Gnanasekaran R, Leitner DM (2012) Analysis of water and hydrogen bond dynamics at the surface of an antifreeze protein. J At Mol Phys 2012:e125071. https:\/\/doi.org\/10.1155\/2012\/125071","journal-title":"J At Mol Phys"},{"issue":"1","key":"10705_CR59","doi-asserted-by":"publisher","first-page":"014101","DOI":"10.1063\/1.2408420","volume":"126","author":"G Bussi","year":"2007","unstructured":"Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126(1):014101. https:\/\/doi.org\/10.1063\/1.2408420","journal-title":"J Chem Phys"},{"issue":"12","key":"10705_CR60","doi-asserted-by":"publisher","first-page":"7182","DOI":"10.1063\/1.328693","volume":"52","author":"M Parrinello","year":"1981","unstructured":"Parrinello M, Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52(12):7182\u20137190. https:\/\/doi.org\/10.1063\/1.328693","journal-title":"J Appl Phys"},{"issue":"10","key":"10705_CR61","doi-asserted-by":"publisher","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","volume":"17","author":"MS Vald\u00e9s-Tresanco","year":"2021","unstructured":"Vald\u00e9s-Tresanco MS, Vald\u00e9s-Tresanco ME, Valiente PA, Moreno E (2021) gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS. J Chem Theory Comput 17(10):6281\u20136291. https:\/\/doi.org\/10.1021\/acs.jctc.1c00645","journal-title":"J Chem Theory Comput"},{"issue":"9","key":"10705_CR62","doi-asserted-by":"publisher","first-page":"3314","DOI":"10.1021\/ct300418h","volume":"8","author":"BRI Miller","year":"2012","unstructured":"Miller BRI, McGee TD Jr, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8(9):3314\u20133321. https:\/\/doi.org\/10.1021\/ct300418h","journal-title":"J Chem Theory Comput"},{"issue":"10","key":"10705_CR63","doi-asserted-by":"publisher","first-page":"2778","DOI":"10.1021\/ci200227u","volume":"51","author":"RA Laskowski","year":"2011","unstructured":"Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand-protein interaction diagrams for drug discovery. J Chem Inf Model 51(10):2778\u20132786. https:\/\/doi.org\/10.1021\/ci200227u","journal-title":"J Chem Inf Model"},{"issue":"1","key":"10705_CR64","doi-asserted-by":"publisher","first-page":"42717","DOI":"10.1038\/srep42717","volume":"7","author":"A Daina","year":"2017","unstructured":"Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7(1):42717. https:\/\/doi.org\/10.1038\/srep42717","journal-title":"Sci Rep"},{"key":"10705_CR65","doi-asserted-by":"publisher","first-page":"W257","DOI":"10.1093\/nar\/gky318","volume":"46","author":"P Banerjee","year":"2018","unstructured":"Banerjee P, Eckert AO, Schrey AK, Preissner R (2018) ProTox-II: a webserver for the prediction of toxicity of chemicals. Nucleic Acids Res 46:W257\u2013W263. https:\/\/doi.org\/10.1093\/nar\/gky318","journal-title":"Nucleic Acids Res"}],"container-title":["Molecular Diversity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-023-10705-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11030-023-10705-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11030-023-10705-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,2]],"date-time":"2024-12-02T14:22:21Z","timestamp":1733149341000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s11030-023-10705-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,2]]},"references-count":65,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2024,10]]}},"alternative-id":["10705"],"URL":"https:\/\/doi.org\/10.1007\/s11030-023-10705-8","relation":{},"ISSN":["1381-1991","1573-501X"],"issn-type":[{"value":"1381-1991","type":"print"},{"value":"1573-501X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,2]]},"assertion":[{"value":"15 January 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 July 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 August 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"None.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"None to declare.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}]}}