{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T21:31:35Z","timestamp":1790544695834,"version":"4.1.0"},"reference-count":59,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T00:00:00Z","timestamp":1621814400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T00:00:00Z","timestamp":1621814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100007943","name":"Graduate School, Kasetsart University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007943","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004704","name":"National Research Council of Thailand","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004704","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004539","name":"Kasetsart University","doi-asserted-by":"publisher","award":["Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries"],"award-info":[{"award-number":["Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries"]}],"id":[{"id":"10.13039\/501100004539","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005621","name":"Kasetsart University Research and Development Institute","doi-asserted-by":"publisher","award":["KURDI(FF(KU)25.64"],"award-info":[{"award-number":["KURDI(FF(KU)25.64"]}],"id":[{"id":"10.13039\/501100005621","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2021,6]]},"DOI":"10.1007\/s00894-021-04798-x","type":"journal-article","created":{"date-parts":[[2021,5,24]],"date-time":"2021-05-24T18:03:12Z","timestamp":1621879392000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["In silico structural elucidation of the rabies RNA-dependent RNA polymerase (RdRp) toward the identification of potential rabies virus inhibitors"],"prefix":"10.1007","volume":"27","author":[{"given":"Duangnapa","family":"Kiriwan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2421-7859","authenticated-orcid":false,"given":"Kiattawee","family":"Choowongkomon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,24]]},"reference":[{"issue":"2","key":"4798_CR1","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1016\/j.virusres.2005.04.004","volume":"111","author":"S Finke","year":"2005","unstructured":"Finke S, Conzelmann K-K (2005) Replication strategies of rabies virus. Virus Res 111(2):120\u2013131. https:\/\/doi.org\/10.1016\/j.virusres.2005.04.004","journal-title":"Virus Res"},{"key":"4798_CR2","unstructured":"Owens, Flores, Di Serio F, Li S, Pall\u00e1s V, Randles J, Sano V (2012) Virus taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. In. pp 1221\u20131234"},{"key":"4798_CR3","unstructured":"Rupprecht CE (1996) Rhabdoviruses: rabies virus. In: th, baron S (eds) medical microbiology. Galveston (TX),"},{"issue":"11","key":"4798_CR4","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1038\/nrd1549","volume":"3","author":"DB Kitchen","year":"2004","unstructured":"Kitchen DB, Decornez H, Furr JR, Bajorath J (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11):935\u2013949. https:\/\/doi.org\/10.1038\/nrd1549","journal-title":"Nat Rev Drug Discov"},{"key":"4798_CR5","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1007\/978-1-4939-7201-2_18","volume":"1647","author":"M Kontoyianni","year":"2017","unstructured":"Kontoyianni M (2017) Docking and virtual screening in drug discovery. Methods Mol Biol 1647:255\u2013266. https:\/\/doi.org\/10.1007\/978-1-4939-7201-2_18","journal-title":"Methods Mol Biol"},{"issue":"1","key":"4798_CR6","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1080\/17460441.2018.1403419","volume":"13","author":"X Liu","year":"2018","unstructured":"Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X (2018) Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discovery 13(1):23\u201337. https:\/\/doi.org\/10.1080\/17460441.2018.1403419","journal-title":"Expert Opin Drug Discovery"},{"issue":"6294","key":"4798_CR7","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/347631a0","volume":"347","author":"M Karplus","year":"1990","unstructured":"Karplus M, Petsko GA (1990) Molecular dynamics simulations in biology. Nature 347(6294):631\u2013639. https:\/\/doi.org\/10.1038\/347631a0","journal-title":"Nature"},{"issue":"7","key":"4798_CR8","doi-asserted-by":"publisher","first-page":"509","DOI":"10.2174\/1381612013397861","volume":"7","author":"T Langer","year":"2001","unstructured":"Langer T, Hoffmann RD (2001) Virtual screening: an effective tool for lead structure discovery? Curr Pharm Des 7(7):509\u2013527. https:\/\/doi.org\/10.2174\/1381612013397861","journal-title":"Curr Pharm Des"},{"issue":"17","key":"4798_CR9","doi-asserted-by":"publisher","first-page":"3203","DOI":"10.1021\/jm990154t","volume":"42","author":"AK Debnath","year":"1999","unstructured":"Debnath AK, Radigan L, Jiang S (1999) Structure-based identification of small molecule antiviral compounds targeted to the gp41 core structure of the human immunodeficiency virus type 1. J Med Chem 42(17):3203\u20133209. https:\/\/doi.org\/10.1021\/jm990154t","journal-title":"J Med Chem"},{"issue":"9","key":"4798_CR10","doi-asserted-by":"publisher","first-page":"4867","DOI":"10.1021\/acs.jmedchem.0c00202","volume":"63","author":"AK Ghosh","year":"2020","unstructured":"Ghosh AK, Kovela S, Osswald HL, Amano M, Aoki M, Agniswamy J, Wang YF, Weber IT, Mitsuya H (2020) Structure-based design of highly potent HIV-1 protease inhibitors containing new tricyclic ring P2-ligands: design, synthesis, biological, and X-ray structural studies. J Med Chem 63(9):4867\u20134879. https:\/\/doi.org\/10.1021\/acs.jmedchem.0c00202","journal-title":"J Med Chem"},{"issue":"2","key":"4798_CR11","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/j.apsb.2019.09.007","volume":"10","author":"K Jin","year":"2020","unstructured":"Jin K, Liu M, Zhuang C, De Clercq E, Pannecouque C, Meng G, Chen F (2020) Improving the positional adaptability: structure-based design of biphenyl-substituted diaryltriazines as novel non-nucleoside HIV-1 reverse transcriptase inhibitors. Acta Pharm Sin B 10(2):344\u2013357. https:\/\/doi.org\/10.1016\/j.apsb.2019.09.007","journal-title":"Acta Pharm Sin B"},{"issue":"2","key":"4798_CR12","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.jsb.2019.05.001","volume":"207","author":"G Song","year":"2019","unstructured":"Song G (2019) Structure-based insights into the mechanism of nucleotide import by HIV-1 capsid. J Struct Biol 207(2):123\u2013135. https:\/\/doi.org\/10.1016\/j.jsb.2019.05.001","journal-title":"J Struct Biol"},{"issue":"31","key":"4798_CR13","doi-asserted-by":"publisher","first-page":"2664","DOI":"10.2174\/1568026619666190119143239","volume":"18","author":"M Kaur","year":"2018","unstructured":"Kaur M, Rawal RK, Rath G, Goyal AK (2018) Structure based drug design: clinically relevant HIV-1 integrase inhibitors. Curr Top Med Chem 18(31):2664\u20132680. https:\/\/doi.org\/10.2174\/1568026619666190119143239","journal-title":"Curr Top Med Chem"},{"key":"4798_CR14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ejmech.2018.10.029","volume":"161","author":"G Costa","year":"2019","unstructured":"Costa G, Rocca R, Corona A, Grandi N, Moraca F, Romeo I, Talarico C, Gagliardi MG, Ambrosio FA, Ortuso F, Alcaro S, Distinto S, Maccioni E, Tramontano E, Artese A (2019) Novel natural non-nucleoside inhibitors of HIV-1 reverse transcriptase identified by shape- and structure-based virtual screening techniques. Eur J Med Chem 161:1\u201310. https:\/\/doi.org\/10.1016\/j.ejmech.2018.10.029","journal-title":"Eur J Med Chem"},{"issue":"1","key":"4798_CR15","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1080\/10799893.2017.1414844","volume":"38","author":"F Shiri","year":"2018","unstructured":"Shiri F, Pirhadi S, Rahmani A (2018) Identification of new potential HIV-1 reverse transcriptase inhibitors by QSAR modeling and structure-based virtual screening. J Recept Signal Transduct Res 38(1):37\u201347. https:\/\/doi.org\/10.1080\/10799893.2017.1414844","journal-title":"J Recept Signal Transduct Res"},{"key":"4798_CR16","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/j.compbiolchem.2017.11.006","volume":"72","author":"AT Onawole","year":"2018","unstructured":"Onawole AT, Kolapo TU, Sulaiman KO, Adegoke RO (2018) Structure based virtual screening of the Ebola virus trimeric glycoprotein using consensus scoring. Comput Biol Chem 72:170\u2013180. https:\/\/doi.org\/10.1016\/j.compbiolchem.2017.11.006","journal-title":"Comput Biol Chem"},{"key":"4798_CR17","doi-asserted-by":"publisher","unstructured":"Bharadwaj S, Rao AK, Dwivedi VD, Mishra SK, Yadava U (2020) Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM\/MM affinity estimation. J Biomol Struct Dyn:1\u201314. https:\/\/doi.org\/10.1080\/07391102.2020.1747545","DOI":"10.1080\/07391102.2020.1747545"},{"key":"4798_CR18","doi-asserted-by":"publisher","unstructured":"Santos FRS, Nunes DAF, Lima WG, Davyt D, Santos LL, Taranto AG, J MSF (2020) Identification of Zika virus NS2B-NS3 protease inhibitors by structure-based virtual screening and drug repurposing approaches. J Chem Inf Model 60 (2):731\u2013737. https:\/\/doi.org\/10.1021\/acs.jcim.9b00933","DOI":"10.1021\/acs.jcim.9b00933"},{"key":"4798_CR19","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1016\/j.ejmech.2018.07.014","volume":"156","author":"A Qadir","year":"2018","unstructured":"Qadir A, Riaz M, Saeed M, Shahzad-Ul-Hussan S (2018) Potential targets for therapeutic intervention and structure based vaccine design against Zika virus. Eur J Med Chem 156:444\u2013460. https:\/\/doi.org\/10.1016\/j.ejmech.2018.07.014","journal-title":"Eur J Med Chem"},{"key":"4798_CR20","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.antiviral.2017.07.007","volume":"145","author":"S Yuan","year":"2017","unstructured":"Yuan S, Chan JF, den-Haan H, Chik KK, Zhang AJ, Chan CC, Poon VK, Yip CC, Mak WW, Zhu Z, Zou Z, Tee KM, Cai JP, Chan KH, de la Pena J, Perez-Sanchez H, Ceron-Carrasco JP, Yuen KY (2017) Structure-based discovery of clinically approved drugs as Zika virus NS2B-NS3 protease inhibitors that potently inhibit Zika virus infection in vitro and in vivo. Antivir Res 145:33\u201343. https:\/\/doi.org\/10.1016\/j.antiviral.2017.07.007","journal-title":"Antivir Res"},{"key":"4798_CR21","doi-asserted-by":"publisher","unstructured":"Anasir MI, Ramanathan B, Poh CL (2020) Structure-based design of antivirals against envelope glycoprotein of dengue virus. Viruses 12(4). https:\/\/doi.org\/10.3390\/v12040367","DOI":"10.3390\/v12040367"},{"issue":"4","key":"4798_CR22","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1016\/j.cell.2020.03.061","volume":"181","author":"JM Wandzik","year":"2020","unstructured":"Wandzik JM, Kouba T, Karuppasamy M, Pflug A, Drncova P, Provaznik J, Azevedo N, Cusack S (2020) A structure-based model for the complete transcription cycle of influenza polymerase. Cell 181(4):877\u2013893 e821. https:\/\/doi.org\/10.1016\/j.cell.2020.03.061","journal-title":"Cell"},{"key":"4798_CR23","doi-asserted-by":"publisher","first-page":"107241","DOI":"10.1016\/j.compbiolchem.2020.107241","volume":"85","author":"Z Jin","year":"2020","unstructured":"Jin Z, Wang Y, Yu XF, Tan QQ, Liang SS, Li T, Zhang H, Shaw PC, Wang J, Hu C (2020) Structure-based virtual screening of influenza virus RNA polymerase inhibitors from natural compounds: molecular dynamics simulation and MM-GBSA calculation. Comput Biol Chem 85:107241. https:\/\/doi.org\/10.1016\/j.compbiolchem.2020.107241","journal-title":"Comput Biol Chem"},{"key":"4798_CR24","doi-asserted-by":"publisher","unstructured":"Zang Y, Hao D, Wang H, Yang Z, Liu H, Zhang S (2019) Structure-based methoxyflavone derivatives with potent inhibitory activity against various influenza neuraminidases. J Biomol Struct Dyn:1\u20138. https:\/\/doi.org\/10.1080\/07391102.2019.1680436","DOI":"10.1080\/07391102.2019.1680436"},{"issue":"5","key":"4798_CR25","doi-asserted-by":"publisher","first-page":"2231","DOI":"10.1128\/AAC.02335-12","volume":"57","author":"N Lejal","year":"2013","unstructured":"Lejal N, Tarus B, Bouguyon E, Chenavas S, Bertho N, Delmas B, Ruigrok RW, Di Primo C, Slama-Schwok A (2013) Structure-based discovery of the novel antiviral properties of naproxen against the nucleoprotein of influenza A virus. Antimicrob Agents Chemother 57(5):2231\u20132242. https:\/\/doi.org\/10.1128\/AAC.02335-12","journal-title":"Antimicrob Agents Chemother"},{"issue":"2","key":"4798_CR26","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.bbagen.2011.11.003","volume":"1820","author":"M Fukuoka","year":"2012","unstructured":"Fukuoka M, Minakuchi M, Kawaguchi A, Nagata K, Kamatari YO, Kuwata K (2012) Structure-based discovery of anti-influenza virus A compounds among medicines. Biochim Biophys Acta 1820(2):90\u201395. https:\/\/doi.org\/10.1016\/j.bbagen.2011.11.003","journal-title":"Biochim Biophys Acta"},{"key":"4798_CR27","doi-asserted-by":"publisher","DOI":"10.1371\/currents.RRN1253","volume":"3","author":"P Fedichev","year":"2011","unstructured":"Fedichev P, Timakhov R, Pyrkov T, Getmantsev E, Vinnik A (2011) Structure-based drug design of a new chemical class of small molecules active against influenza A nucleoprotein in vitro and in vivo. PLoS Curr 3:RRN1253. https:\/\/doi.org\/10.1371\/currents.RRN1253","journal-title":"PLoS Curr"},{"issue":"3","key":"4798_CR28","doi-asserted-by":"publisher","first-page":"315","DOI":"10.2174\/138945010790711932","volume":"11","author":"PM Mitrasinovic","year":"2010","unstructured":"Mitrasinovic PM (2010) Advances in the structure-based design of the influenza A neuraminidase inhibitors. Curr Drug Targets 11(3):315\u2013326. https:\/\/doi.org\/10.2174\/138945010790711932","journal-title":"Curr Drug Targets"},{"issue":"1\u20133","key":"4798_CR29","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.bpc.2008.11.004","volume":"140","author":"PM Mitrasinovic","year":"2009","unstructured":"Mitrasinovic PM (2009) On the structure-based design of novel inhibitors of H5N1 influenza A virus neuraminidase (NA). Biophys Chem 140(1\u20133):35\u201338. https:\/\/doi.org\/10.1016\/j.bpc.2008.11.004","journal-title":"Biophys Chem"},{"issue":"12","key":"4798_CR30","doi-asserted-by":"publisher","first-page":"3980","DOI":"10.1021\/jm049276y","volume":"48","author":"CJ Maring","year":"2005","unstructured":"Maring CJ, Stoll VS, Zhao C, Sun M, Krueger AC, Stewart KD, Madigan DL, Kati WM, Xu Y, Carrick RJ, Montgomery DA, Kempf-Grote A, Marsh KC, Molla A, Steffy KR, Sham HL, Laver WG, Gu YG, Kempf DJ, Kohlbrenner WE (2005) Structure-based characterization and optimization of novel hydrophobic binding interactions in a series of pyrrolidine influenza neuraminidase inhibitors. J Med Chem 48(12):3980\u20133990. https:\/\/doi.org\/10.1021\/jm049276y","journal-title":"J Med Chem"},{"issue":"5","key":"4798_CR31","doi-asserted-by":"publisher","first-page":"1849","DOI":"10.1021\/ci049844i","volume":"44","author":"T Steindl","year":"2004","unstructured":"Steindl T, Langer T (2004) Influenza virus neuraminidase inhibitors: generation and comparison of structure-based and common feature pharmacophore hypotheses and their application in virtual screening. J Chem Inf Comput Sci 44(5):1849\u20131856. https:\/\/doi.org\/10.1021\/ci049844i","journal-title":"J Chem Inf Comput Sci"},{"issue":"3","key":"4798_CR32","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1021\/bi0205449","volume":"42","author":"V Stoll","year":"2003","unstructured":"Stoll V, Stewart KD, Maring CJ, Muchmore S, Giranda V, Gu YG, Wang G, Chen Y, Sun M, Zhao C, Kennedy AL, Madigan DL, Xu Y, Saldivar A, Kati W, Laver G, Sowin T, Sham HL, Greer J, Kempf D (2003) Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series. Biochemistry 42(3):718\u2013727. https:\/\/doi.org\/10.1021\/bi0205449","journal-title":"Biochemistry"},{"issue":"11","key":"4798_CR33","doi-asserted-by":"publisher","first-page":"8808","DOI":"10.1128\/jvi.71.11.8808-8820.1997","volume":"71","author":"LR Hoffman","year":"1997","unstructured":"Hoffman LR, Kuntz ID, White JM (1997) Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity. J Virol 71(11):8808\u20138820","journal-title":"J Virol"},{"issue":"17","key":"4798_CR34","doi-asserted-by":"publisher","first-page":"3217","DOI":"10.1021\/jm00017a005","volume":"38","author":"S Singh","year":"1995","unstructured":"Singh S, Jedrzejas MJ, Air GM, Luo M, Laver WG, Brouillette WJ (1995) Structure-based inhibitors of influenza virus sialidase. A benzoic acid lead with novel interaction. J Med Chem 38(17):3217\u20133225. https:\/\/doi.org\/10.1021\/jm00017a005","journal-title":"J Med Chem"},{"key":"4798_CR35","doi-asserted-by":"publisher","unstructured":"Dai W, Zhang B, Su H, Li J, Zhao Y, Xie X, Jin Z, Liu F, Li C, Li Y, Bai F, Wang H, Cheng X, Cen X, Hu S, Yang X, Wang J, Liu X, Xiao G, Jiang H, Rao Z, Zhang LK, Xu Y, Yang H, Liu H (2020) Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease. Science. https:\/\/doi.org\/10.1126\/science.abb4489","DOI":"10.1126\/science.abb4489"},{"issue":"2","key":"4798_CR36","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/0042-6822(88)90600-9","volume":"165","author":"N Tordo","year":"1988","unstructured":"Tordo N, Poch O, Ermine A, Keith G, Rougeon F (1988) Completion of the rabies virus genome sequence determination: highly conserved domains among the L (polymerase) proteins of unsegmented negative-strand RNA viruses. Virology 165(2):565\u2013576. https:\/\/doi.org\/10.1016\/0042-6822(88)90600-9","journal-title":"Virology"},{"issue":"11","key":"4798_CR37","doi-asserted-by":"publisher","first-page":"5823","DOI":"10.1021\/acs.jctc.8b00758","volume":"14","author":"TFD Silva","year":"2018","unstructured":"Silva TFD, Vila-Vicosa D, Reis P, Victor BL, Diem M, Oostenbrink C, Machuqueiro M (2018) The impact of using single atomistic long-range cutoff schemes with the GROMOS 54A7 force field. J Chem Theory Comput 14(11):5823\u20135833. https:\/\/doi.org\/10.1021\/acs.jctc.8b00758","journal-title":"J Chem Theory Comput"},{"key":"4798_CR38","unstructured":"Turner P (2005) XMGRACE, version 5.1. 19. Center for Coastal and Land-Margin Research, Oregon graduate Institute of Science and Technology, Beaverton, OR"},{"issue":"4","key":"4798_CR39","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1007\/bf00228148","volume":"8","author":"RA Laskowski","year":"1996","unstructured":"Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8(4):477\u2013486. https:\/\/doi.org\/10.1007\/bf00228148","journal-title":"J Biomol NMR"},{"key":"4798_CR40","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1109\/ICCABS.2011.5729867","volume":"2011","author":"N Alexander","year":"2011","unstructured":"Alexander N, Woetzel N, Meiler J (2011) Bcl::cluster : a method for clustering biological molecules coupled with visualization in the pymol molecular graphics system. IEEE Int Conf Comput Adv Bio Med Sci 2011:13\u201318. https:\/\/doi.org\/10.1109\/ICCABS.2011.5729867","journal-title":"IEEE Int Conf Comput Adv Bio Med Sci"},{"issue":"5","key":"4798_CR41","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1038\/nprot.2015.043","volume":"10","author":"D Kozakov","year":"2015","unstructured":"Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE, Luo L, Xia B, Beglov D, Vajda S (2015) The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nat Protoc 10(5):733\u2013755. https:\/\/doi.org\/10.1038\/nprot.2015.043","journal-title":"Nat Protoc"},{"issue":"8","key":"4798_CR42","doi-asserted-by":"publisher","first-page":"1511","DOI":"10.1038\/nprot.2012.085","volume":"7","author":"M K\u00e4llberg","year":"2012","unstructured":"K\u00e4llberg M, Wang H, Wang S, Peng J, Wang Z, Lu H, Xu J (2012) Template-based protein structure modeling using the RaptorX web server. Nat Protoc 7(8):1511\u20131522. https:\/\/doi.org\/10.1038\/nprot.2012.085","journal-title":"Nat Protoc"},{"issue":"W1","key":"4798_CR43","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":"1","key":"4798_CR44","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/S0022-2836(95)80037-9","volume":"245","author":"G Jones","year":"1995","unstructured":"Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245(1):43\u201353. https:\/\/doi.org\/10.1016\/S0022-2836(95)80037-9","journal-title":"J Mol Biol"},{"issue":"6","key":"4798_CR45","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1007\/s10822-012-9551-4","volume":"26","author":"JW Liebeschuetz","year":"2012","unstructured":"Liebeschuetz JW, Cole JC, Korb O (2012) Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test. J Comput Aided Mol Des 26(6):737\u2013748. https:\/\/doi.org\/10.1007\/s10822-012-9551-4","journal-title":"J Comput Aided Mol Des"},{"issue":"1","key":"4798_CR46","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1021\/ci049714+","volume":"45","author":"JJ Irwin","year":"2005","unstructured":"Irwin JJ, Shoichet BK (2005) ZINC \u2212 a free database of commercially available compounds for virtual screening. J Chem Inf Model 45(1):177\u2013182. https:\/\/doi.org\/10.1021\/ci049714+","journal-title":"J Chem Inf Model"},{"issue":"3","key":"4798_CR47","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":"Pt 8","key":"4798_CR48","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1107\/S0907444904011679","volume":"60","author":"AW Schuttelkopf","year":"2004","unstructured":"Schuttelkopf AW, van Aalten DM (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 60(Pt 8):1355\u20131363. https:\/\/doi.org\/10.1107\/S0907444904011679","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"issue":"7","key":"4798_CR49","doi-asserted-by":"publisher","first-page":"1951","DOI":"10.1021\/ci500020m","volume":"54","author":"R Kumari","year":"2014","unstructured":"Kumari R, Kumar R, Open Source Drug Discovery C, Lynn A (2014) g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 54(7):1951\u20131962. https:\/\/doi.org\/10.1021\/ci500020m","journal-title":"J Chem Inf Model"},{"issue":"13","key":"4798_CR50","doi-asserted-by":"publisher","first-page":"3381","DOI":"10.1093\/nar\/gkg520","volume":"31","author":"T Schwede","year":"2003","unstructured":"Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 31(13):3381\u20133385","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"4798_CR51","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.cell.2015.06.018","volume":"162","author":"B Liang","year":"2015","unstructured":"Liang B, Li Z, Jenni S, Rahmeh AA, Morin BM, Grant T, Grigorieff N, Harrison SC, Whelan SPJ (2015) Structure of the L protein of vesicular stomatitis virus from electron cryomicroscopy. Cell 162(2):314\u2013327. https:\/\/doi.org\/10.1016\/j.cell.2015.06.018","journal-title":"Cell"},{"key":"4798_CR52","doi-asserted-by":"publisher","first-page":"3867","DOI":"10.1002\/j.1460-2075.1989.tb08565.x","volume":"8","author":"O Poch","year":"1990","unstructured":"Poch O, Sauvaget I, Delarue M, Tordo N (1990) Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J 8:3867\u20133874. https:\/\/doi.org\/10.1002\/j.1460-2075.1989.tb08565.x","journal-title":"EMBO J"},{"issue":"4","key":"4798_CR53","doi-asserted-by":"publisher","first-page":"827","DOI":"10.1007\/s00705-006-0881-1","volume":"152","author":"DE Magoffin","year":"2006","unstructured":"Magoffin DE, Halpin K, Rota PA, Wang LF (2006) Effects of single amino acid substitutions at the E residue in the conserved GDNE motif of the Nipah virus polymerase (L) protein. Arch Virol 152(4):827. https:\/\/doi.org\/10.1007\/s00705-006-0881-1","journal-title":"Arch Virol"},{"issue":"11","key":"4798_CR54","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1111\/1348-0421.12329","volume":"59","author":"Y Matsumoto","year":"2015","unstructured":"Matsumoto Y, Ohta K, Yumine N, Goto H, Nishio M (2015) Identification of two essential aspartates for polymerase activity in parainfluenza virus L protein by a minireplicon system expressing secretory luciferase. Microbiol Immunol 59(11):676\u2013683. https:\/\/doi.org\/10.1111\/1348-0421.12329","journal-title":"Microbiol Immunol"},{"issue":"20","key":"4798_CR55","doi-asserted-by":"publisher","first-page":"e00826","DOI":"10.1128\/JVI.00826-17","volume":"91","author":"K Nakagawa","year":"2017","unstructured":"Nakagawa K, Kobayashi Y, Ito N, Suzuki Y, Okada K, Makino M, Goto H, Takahashi T, Sugiyama M (2017) Molecular function analysis of rabies virus RNA polymerase L protein by using an L gene-deficient virus. J Virol 91(20):e00826\u2013e00817. https:\/\/doi.org\/10.1128\/JVI.00826-17","journal-title":"J Virol"},{"issue":"3","key":"4798_CR56","doi-asserted-by":"publisher","first-page":"1334","DOI":"10.1128\/JVI.67.3.1334-1339.1993","volume":"67","author":"DE Sleat","year":"1993","unstructured":"Sleat DE, Banerjee AK (1993) Transcriptional activity and mutational analysis of recombinant vesicular stomatitis virus RNA polymerase. J Virol 67(3):1334\u20131339. https:\/\/doi.org\/10.1128\/JVI.67.3.1334-1339.1993","journal-title":"J Virol"},{"issue":"2","key":"4798_CR57","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1006\/viro.1995.0063","volume":"214","author":"MJ Schnell","year":"1995","unstructured":"Schnell MJ, Conzelmann K-K (1995) Polymerase activity ofin vitromutated rabies virus L protein. Virology 214(2):522\u2013530. https:\/\/doi.org\/10.1006\/viro.1995.0063","journal-title":"Virology"},{"issue":"3","key":"4798_CR58","first-page":"93","volume":"10","author":"AG Malur","year":"2002","unstructured":"Malur AG, Gupta NK, De Bishnu P, Banerjee AK (2002) Analysis of the mutations in the active site of the RNA-dependent RNA polymerase of human parainfluenza virus type 3 (HPIV3). Gene Expr 10(3):93\u2013100","journal-title":"Gene Expr"},{"issue":"2","key":"4798_CR59","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.virusres.2003.11.003","volume":"99","author":"A Chattopadhyay","year":"2004","unstructured":"Chattopadhyay A, Raha T, Shaila MS (2004) Effect of single amino acid mutations in the conserved GDNQ motif of L protein of rinderpest virus on RNA synthesis in vitro and in vivo. Virus Res 99(2):139\u2013145. https:\/\/doi.org\/10.1016\/j.virusres.2003.11.003","journal-title":"Virus Res"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-021-04798-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00894-021-04798-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-021-04798-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T09:01:49Z","timestamp":1744189309000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00894-021-04798-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,24]]},"references-count":59,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2021,6]]}},"alternative-id":["4798"],"URL":"https:\/\/doi.org\/10.1007\/s00894-021-04798-x","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,24]]},"assertion":[{"value":"26 June 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 May 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that they have no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"183"}}