References
- Ahmad, R. (2019). Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: An in silico analysis. Peer Journal, 7, e6012. https://doi.org/https://doi.org/10.7717/peerj.6012
- Ames, B. N., McCann, J., & Yamasaki, E. (1975). Methods for detecting carcinogens and mutagens with the Salmonella/mammalian–microsome mutagenicity test. Mutation Research/Environmental Mutagenesis & Related Subjects, 31(6), 347–363.
- Anand, K., Ziebuhr, J., Wadhwani, P., Mesters, J. R., & Hilgenfeld, R. (2003). Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science (New York, NY), 300(5626), 1763–1767. https://doi.org/https://doi.org/10.1126/science.1085658
- Aniyery, R. B., Gupta, A., Singh, P., Khatri, C., & Pathak, A. (2015). Synthesis, characterization, biological activities and computational anticancer study of Dibutylbis [(2-isopropyl-5-ethylcyclohexyl) oxy] stannane. Journal of Chemical & Pharmaceutical Science, 8, 957–963.
- Arya, R., Das, A., Prashar, V., & Kumar, M. (2010). Potential inhibitors against papain-like protease of novel coronavirus (SARS-CoV-2) from FDA approved drugs. ChemRxiv. Preprint. https://doi.org/https://doi.org/10.26434/chemrxiv.11860011.v2
- Báez-Santos, Y. M., John, S. E., & Mesecar, A. D. (2015). The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds. Antiviral Research, 115, 21–38. https://doi.org/https://doi.org/10.1016/j.antiviral.2014.12.015
- Bahar, I., Lezon, T. R., Bakan, A., & Shrivastava, I. H. (2010). Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins. Chemical Reviews, 110(3), 1463–1497. https://doi.org/https://doi.org/10.1021/cr900095e
- Balakrishnan, N. A., Raj, J. S., & Kandakatla, N. A. (2015). In silico studies on new indazole derivatives as gsk-3 β inhibitors. International Journal of Pharmacy & Pharmaceutical Sciences, 7, 295–299.
- Balakrishnan, N., Raj, J. S., & Kandakatla, N. (2014). 2D/3D-QSAR, docking and optimization of 5-substituted-1h-indazole as inhibitors of GSK-3β. International Journal of Pharmaceutical Science, 6(10), 413–420.
- Belouzard, S., Chu, V. C., & Whittaker, G. R. (2009). Activation of the SARS coronavirus spike protein via sequential proteolytic cleavage at two distinct sites. Proceedings of the National Academy of Sciences of the United States of America, 106(14), 5871–5876. https://doi.org/https://doi.org/10.1073/pnas.0809524106
- Bosch, B. J., van der Zee, R., de Haan, C. A., & Rottier, P. J. (2003). The coronavirus spike protein is a class I virus fusion protein: Structural and functional characterization of the fusion core complex. Journal of Virology, 77(16), 8801–8811. https://doi.org/https://doi.org/10.1128/jvi.77.16.8801-8811.2003
- Burkard, C., Verheije, M. H., Wicht, O., van Kasteren, S. I., van Kuppeveld, F. J., Haagmans, B. L., Pelkmans, L., Rottier, P. J., Bosch, B. J., & de Haan, C. A. (2014). Coronavirus cell entry occurs through the endo-/lysosomal pathway in a proteolysis-dependent manner. PLoS Pathogens, 10(11), e1004502.
- Cai, Z., Zhang, G., Tang, B., Liu, Y., Fu, X., & Zhang, X. (2015). Promising anti-influenza properties of active constituent of Withania somnifera ayurvedic herb in targeting neuraminidase of H1N1 influenza: Computational study. Cell Biochemistry & Biophysics, 72(3), 727–739. https://doi.org/https://doi.org/10.1007/s12013-015-0524-9
- Campillos, M., Kuhn, M., Gavin, A. C., Jensen, L. J., & Bork, P. (2008). Drug target identification using side-effect similarity. Science (New York, NY), 321(5886), 263–266. https://doi.org/https://doi.org/10.1126/science.1158140
- Chan, J. F. W., Chan, K.-H., Kao, R. Y. T., To, K. K. W., Zheng, B.-J., Li, C. P. Y., Li, P. T. W., Dai, J., Mok, F. K. Y., Chen, H., Hayden, F. G., & Yuen, K.-Y. (2013). Broad-spectrum antivirals for the emerging Middle East respiratory syndrome coronavirus. The Journal of Infection, 67(6), 606–616. https://doi.org/https://doi.org/10.1016/j.jinf.2013.09.029
- Chen, Y., Liu, Q., & Guo, D. (2020). Emerging coronaviruses: Genome structure, replication, and pathogenesis. Journal of Medical Virology, 92(4), 418–423. https://doi.org/https://doi.org/10.1002/jmv.25681
- Chen, Y. W., Yiu, C. P., & Wong, K. Y. (2020). Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: Virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000 Research, 9, 129.
- Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. J. Chem. Inf. Model. 52(11), 3099–3105. https://doi.org/https://doi.org/10.1021/ci300367a
- Cheng, T., Li, Q., Zhou, Z., Wang, Y., & Bryant, S. H. (2012). Structure-based virtual screening for drug discovery: A problem-centric review. The AAPS Journal, 14(1), 133–141. https://doi.org/https://doi.org/10.1208/s12248-012-9322-0
- Coronavirus Outbreak in India. https://www.covid19india.org/.
- de Wilde, A. H., Jochmans, D., Posthuma, C. C., Zevenhoven-Dobbe, J. C., van Nieuwkoop, S., Bestebroer, T. M., van den Hoogen, B. G., Neyts, J., & Snijder, E. J. (2014). Screening of an FDA-approved compound library identifies four small-molecule inhibitors of Middle East respiratory syndrome coronavirus replication in cell culture. Antimicrobial Agents & Chemotherapy, 58(8), 4875–4884. https://doi.org/https://doi.org/10.1128/AAC.03011-14
- Delaney, J. S. (2004). ESOL: Estimating aqueous solubility directly from molecular structure. Journal of Chemical Information & Computer Sciences, 44(3), 1000–1005. https://doi.org/https://doi.org/10.1021/ci034243x
- Dhar, N., Rana, S., Bhat, W. W., Razdan, S., Pandith, S. A., Khan, S., Dutt, P., Dhar, R. S., Vaishnavi, S., Vishwakarma, R., & Lattoo, S. K. (2013). Dynamics of withanolide biosynthesis in relation to temporal expression pattern of metabolic genes in Withania somnifera (L.) Dunal: A comparative study in two morpho-chemovariants. Molecular Biology Reports, 40(12), 7007–7016. https://doi.org/https://doi.org/10.1007/s11033-013-2820-z
- Dhar, N., Razdan, S., Rana, S., Bhat, W. W., Vishwakarma, R., & Lattoo, S. K. (2015). A decade of molecular understanding of withanolide biosynthesis and in vitro studies in Withania somnifera (L.) Dunal: Prospects and perspectives for pathway engineering. Frontiers in Plant Sciences, 6, 1031. https://doi.org/https://doi.org/10.3389/fpls.2015.01031
- Donoghue, M., Hsieh, F., Baronas, E., Godbout, K., Gosselin, M., Stagliano, N., Donovan, M., Woolf, B., Robison, K., Jeyaseelan, R., Breitbart, R. E., & Acton, S. (2000). A novel angiotensin-converting enzyme-related carboxypeptidase (ACE2) converts angiotensin I to angiotensin 1–9. Circulation Research, 87(5), E1. https://doi.org/https://doi.org/10.1161/01.res.87.5.e1
- Dyalla, J., Christopher, M. C., Harta, B. J., Venkataramanb, T., Michael, R., Holbrooka, J. K., Reed, F. J., Gene, G. O., Jr Peter, B. J., Laidlawd, M., & Lisa, M. J. (2014). Repurposing of clinically developed drugs for treatment of Middle East Respiratory Coronavirus Infection 2. Infection, 2, 3.
- Egan, W. J., Merz, K. M., & Baldwin, J. J. (2000). Prediction of drug absorption using multivariate statistics. Journal of Medicinal Chemistry, 43(21), 3867–3877. https://doi.org/https://doi.org/10.1021/jm000292e
- Ertl, P., Rohde, B., & Selzer, P. (2000). Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. Journal of Medicinal Chemistry, 43(20), 3714–3717. https://doi.org/https://doi.org/10.1021/jm000942e
- Fouchier, R. A., Kuiken, T., Schutten, M., Van Amerongen, G., Van Doornum, G. J., Van Den Hoogen, B. G., Peiris, M., Lim, W., Stöhr, K., & Osterhaus, A. D. (2003). Aetiology: Koch's postulates fulfilled for SARS virus. Nature, 423(6937), 240. https://doi.org/https://doi.org/10.1038/423240a
- Galvelis, R., Doerr, S., Damas, J. M., Harvey, M. J., & De Fabritiis, G. (2019). A scalable molecular force field parameterization method based on density functional theory and quantum-level machine learning. Journal of Chemical Information & Modelling, 59(8), 3485–3493. https://doi.org/https://doi.org/10.1021/acs.jcim.9b00439
- Ghose, T. K. (1987). Measurement of cellulase activities. Pure & Applied Chemistry, 59(2), 257–268.
- Ghose, A., & Crippen, G. (1987). Atomic physicochemical parameters for three-dimensional-structure-directed quantitative structure-activity relationships. 2. Modeling dispersive and hydrophobic interactions. Journal of Chemical Information & Computer Sciences, 27(1), 21–35. https://doi.org/https://doi.org/10.1021/ci00053a005
- Ghose, A. K., Viswanadhan, V. N., & Wendoloski, J. J. (1999). A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. Journal of Combinatorial Chemistry, 1(1), 55–68. https://doi.org/https://doi.org/10.1021/cc9800071
- Glass, W. G., Subbarao, K., Murphy, B., & Murphy, P. M. (2004). Mechanisms of host defense following severe acute respiratory syndrome-coronavirus (SARS-CoV) pulmonary infection of mice. Journal of Immunology (Baltimore, MD 1950)), 173(6), 4030–4039. https://doi.org/https://doi.org/10.4049/jimmunol.173.6.4030
- Guy, J. L., Jackson, R. M., Jensen, H. A., Hooper, N. M., & Turner, A. J. (2005). Identification of critical active-site residues in angiotensin-converting enzyme-2 (ACE2) by site-directed mutagenesis. The FEBS Journal, 272(14), 3512–3520. https://doi.org/https://doi.org/10.1111/j.1742-4658.2005.04756.x
- Hamming, I., Timens, W., Bulthuis, M. L., Lely, A. T., Navis, G. J., & van Goor, H. (2004). Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus. A first step in understanding SARS pathogenesis. The Journal of Pathology, 203(2), 631–637. https://doi.org/https://doi.org/10.1002/path.1570
- Harcourt, B. H., Jukneliene, D., Kanjanahaluethai, A., Bechill, J., Severson, K. M., Smith, C. M., Rota, P. A., & Baker, S. C. (2004). Identification of severe acute respiratory syndrome coronavirus replicase products and characterization of papain-like protease activity. Journal of Virology, 78(24), 13600–13612. https://doi.org/https://doi.org/10.1128/JVI.78.24.13600-13612.2004
- Harmer, D., Gilbert, M., Borman, R., & Clark, K. L. (2002). Quantitative mRNA expression profiling of ACE 2, a novel homologue of angiotensin converting enzyme. FEBS Letters, 532(1–2), 107–110.
- Hogan, R. J., Gao, G., Rowe, T., Bell, P., Flieder, D., Paragas, J., Kobinger, G. P., Wivel, N. A., Crystal, R. G., Boyer, J., Feldmann, H., Voss, T. G., & Wilson, J. M. (2004). Resolution of primary severe acute respiratory syndrome-associated coronavirus infection requires Stat1. Journal of Virology, 78(20), 11416–11421. https://doi.org/https://doi.org/10.1128/JVI.78.20.11416-11421.2004
- Jain, R., Kachhwaha, S., & Kothari, S. L. (2012). Phytochemistry, pharmacology, and biotechnology of Withania somnifera and Withania coagulans: A review. Journal of Medicinal Plants Research, 6(41), 5388–5399.
- Khan, T., Ahmad, R., Azad, I., Raza, S., Joshi, S., & Khan, A. R. (2018). Computer-aided drug design and virtual screening of targeted combinatorial libraries of mixed-ligand transition metal complexes of 2-butanone thiosemicarbazone. Computational Biology & Chemistry, 75, 178–195. https://doi.org/https://doi.org/10.1016/j.compbiolchem.2018.05.008
- Kirchdoerfer, R. N., Cottrell, C. A., Wang, N., Pallesen, J., Yassine, H. M., Turner, H. L., Corbett, K. S., Graham, B. S., McLellan, J. S., & Ward, A. B. (2016). Pre-fusion structure of a human coronavirus spike protein. Nature, 531(7592), 118–121. https://doi.org/https://doi.org/10.1038/nature17200
- Kuiken, T., Fouchier, R. A., Schutten, M., Rimmelzwaan, G. F., van Amerongen, G., van Riel, D., Laman, J. D., de Jong, T., van Doornum, G., Lim, W., Ling, A. E., Chan, P. K., Tam, J. S., Zambon, M. C., Gopal, R., Drosten, C., van der Werf, S., Escriou, N., Manuguerra, J.-C., … Osterhaus, A. D. (2003). Osterhaus AD: Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome. Lancet, 362(9380), 263–270.
- Kumar, V., Dey, A., Hadimani, M. B., Marcović, T., & Emerald, M. (2015). Chemistry and pharmacology of Withania somnifera: An update. Tang, 5(1), 1–3.
- Kuzmanic, A., & Zagrovic, B. (2010). Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophysical Journal, 98(5), 861–871.
- Laskowski, R. A., Hutchinson, E. G., Michie, A. D., Wallace, A. C., Jones, M. L., & Thornton, J. M. (1997). PDBsum: A web-based database of summaries and analyses of all PDB structures. Trends in Biochemical Sciences, 22(12), 488–490.
- Li, W., Zhang, C., Sui, J., Kuhn, J. H., Moore, M. J., Luo, S., Wong, S.-K., Huang, I.-C., Xu, K., Vasilieva, N., Murakami, A., He, Y., Marasco, W. A., Guan, Y., Choe, H., & Farzan, M. (2005). Receptor and viral determinants of SARS-coronavirus adaptation to human ACE2. The EMBO Journal, 24(8), 1634–1643. https://doi.org/https://doi.org/10.1038/sj.emboj.7600640
- Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1–3), 3–25.
- Liu, X., Zhang, B., J. Z., Yang, H., & Rao, Z. (2020). The crystal structure of COVID-19 main protease in complex with an inhibitor N3. PDB.
- Liu, S., Zheng, Q., & Wang, Z. (2020). Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus. Bioinformatics (Oxford, England), 36(11), 3295–3298.
- Martin, Y. C. (2005). A bioavailability score. Journal of Medicinal Chemistry, 48(9), 3164–3170.
- Martina, B. E., Haagmans, B. L., Kuiken, T., Fouchier, R. A., Rimmelzwaan, G. F., Van Amerongen, G., Peiris, J. M., Lim, W., & Osterhaus, A. D. (2003). Virology: SARS virus infection of cats and ferrets. Nature, 425(6961), 915. https://doi.org/https://doi.org/10.1038/425915a
- Martínez-Rosell, G., Giorgino, T., & De Fabritiis, G. (2017). PlayMolecule ProteinPrepare: A web application for protein preparation for molecular dynamics simulations. Journal of Chemical Information & Modelling, 57(7), 1511–1516. https://doi.org/https://doi.org/10.1021/acs.jcim.7b00190
- McAuliffe, J., Vogel, L., Roberts, A., Fahle, G., Fischer, S., Shieh, W. J., Butler, E., Zaki, S., Claire, M. S., Murphy, B., & Subbarao, K. (2004). Replication of SARS coronavirus administered into the respiratory tract of African Green, rhesus and cynomolgus monkeys. Virology, 330(1), 8–15. https://doi.org/https://doi.org/10.1016/j.virol.2004.09.030
- Mirjalili, M. H., Moyano, E., Bonfill, M., Cusido, R. M., & Palazón, J. (2009). Steroidal lactones from Withania somnifera, an ancient plant for novel medicine. Molecules (Basel, Switzerland)), 14(7), 2373–2393. https://doi.org/https://doi.org/10.3390/molecules14072373
- Misico, R. I., Nicotra, V. E., Oberti, J. C., Barboza, G., Gil, R. R., & Burton, G. (2011). Withanolides and related steroids. In Progress in the chemistry of organic natural products (Vol. 94, pp. 127–229). Springer.
- Misra, L., Mishra, P., Pandey, A., Sangwan, R. S., Sangwan, N. S., & Tuli, R. (2008). Withanolides from Withania somnifera roots. Phytochemistry, 69(4), 1000–1004. https://doi.org/https://doi.org/10.1016/j.phytochem.2007.10.024
- Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962.
- Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662.
- Mortelmans, K., & Zeiger, E. (2000). The Ames Salmonella/microsome mutagenicity assay. Mutation Research, 455(1–2), 29–60.
- Muegge, I., Heald, S. L., & Brittelli, D. (2001). Simple selection criteria for drug-like chemical matter. Journal of Medicinal Chemistry, 44(12), 1841–1846. https://doi.org/https://doi.org/10.1021/jm015507e
- Nebert, D. W., & Russell, D. W. (2002). Clinical importance of the cytochromes P450. The Lancet, 360(9340), 1155–1162.
- New drug target found for COVID-19. (2020). Argonne National Laboratory [Internet]. Anl.gov. [cited 1 June 2020]. https://www.anl.gov/article/new-drug-target-found-for-covid19
- Oprea, T. I., Davis, A. M., Teague, S. J., & Leeson, P. D. (2001). Is there a difference between leads and drugs? A historical perspective. Journal of Chemical Information & Computer Sciences, 41(5), 1308–1315. https://doi.org/https://doi.org/10.1021/ci010366a
- Proudfoot, A. E. (2002). Chemokine receptors: Multifaceted therapeutic targets. Nature Reviews. Immunology, 2(2), 106–115. https://doi.org/https://doi.org/10.1038/nri722
- Richman, D. D., Whitley, R. J., & Hayden, F. G. (2016). Clinical virology. John Wiley & Sons.
- Roberts, A., Vogel, L., Guarner, J., Hayes, N., Murphy, B., Zaki, S., & Subbarao, K. (2005). Severe acute respiratory syndrome coronavirus infection of golden Syrian hamsters. Journal of Virology, 79(1), 503–511. https://doi.org/https://doi.org/10.1128/JVI.79.1.503-511.2005
- Rowe, T., Gao, G., Hogan, R. J., Crystal, R. G., Voss, T. G., Grant, R. L., Bell, P., Kobinger, G. P., Wivel, N. A., & Wilson, J. M. (2004). Macaque model for severe acute respiratory syndrome. Journal of Virology, 78(20), 11401–11404. https://doi.org/https://doi.org/10.1128/JVI.78.20.11401-11404.2004
- Sander, T. (2001). OSIRIS property explorer. Organic Chemistry Portal.
- Sangwan, R., Chaurasiya, N., Lal, P., Misra, L., Tuli, R., & Sangwan, N. (2008). Withanolide A is inherently de novo biosynthesized in roots of the medicinal plant Ashwagandha (Withania somnifera). Physiologia Plantarum, 133(2), 278–287. https://doi.org/https://doi.org/10.1111/j.1399-3054.2008.01076.x
- Teague, S. J., Davis, A. M., Leeson, P. D., & Oprea, T. (1999). The design of leadlike combinatorial libraries. Angewandte Chemie International Edition, 38(24), 3743–3748.
- Tian, S., Wang, J., Li, Y., Li, D., Xu, L., & Hou, T. (2015). The application of in silico drug-likeness predictions in pharmaceutical research. Advanced Drug Delivery Reviews, 86, 2–10. https://doi.org/https://doi.org/10.1016/j.addr.2015.01.009
- Tortorici, M. A., & Veesler, D. (2019). Structural insights into coronavirus entry. Advances in Virus Research, 105, 93–116. https://doi.org/https://doi.org/10.1016/bs.aivir.2019.08.002
- Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/https://doi.org/10.1002/jcc.21334
- van Breemen, R. B., & Li, Y. (2005). Caco-2 cell permeability assays to measure drug absorption. Expert Opinion on Drug Metabolism & Toxicology, 1(2), 175–185. https://doi.org/https://doi.org/10.1517/17425255.1.2.175
- Varshney, A., Balkrishna, A., & Singh, J. (2020).Withanone from Withania somnifera may inhibit novel coronavirus (COVID-19) entry by disrupting interactions between viral s-protein receptor binding domain and host ACE2 receptor. Virology. https://doi.org/https://doi.org/10.21203/rs.3.rs-17806/v1
- Veber, D. F., Johnson, S. R., Cheng, H. Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. https://doi.org/https://doi.org/10.1021/jm020017n
- Viswanadhan, V. N., Denckla, B., & Weinstein, J. N. (1991). New joint prediction algorithm (Q7-JASEP) improves the prediction of protein secondary structure. Biochemistry, 30(46), 11164–11172. https://doi.org/https://doi.org/10.1021/bi00110a021
- Viswanadhan, V. N., Ghose, A. K., & Weinstein, J. N. (1990). Mapping the binding site of the nucleoside transporter protein: A 3D-QSAR study. Biochimica et Biophysica Acta (BBA)-Protein Structure & Molecular Enzymology, 1039(3), 356–366.
- Wang, Z., Chen, X., Lu, Y., Chen, F., & Zhang, W. (2020). Clinical characteristics and therapeutic procedure for four cases with 2019 novel coronavirus pneumonia receiving combined Chinese and Western medicine treatment. BioScience Trends, 14(1), 64–68.
- Wirth, M., & Sauer, W. H. (2011). Bioactive molecules: perfectly shaped for their target? Molecular Informatics, 30(8), 677–688. https://doi.org/https://doi.org/10.1002/minf.201100034
- Worldometer. (2020). https://www.worldometers.info/coronavirus/.
- Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., & Zheng, M. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharm Sin B. 10(5), 766-788.
- Xu, C., Cheng, F., Chen, L., Du, Z., Li, W., Liu, G., Lee, P. W., & Tang, Y. (2012). In silico prediction of chemical Ames mutagenicity. Journal of Chemical Information & Modeling, 52(11), 2840–2847. https://doi.org/https://doi.org/10.1021/ci300400a
- Yang, J. M., & Chen, C. C. (2004). GEMDOCK: A generic evolutionary method for molecular docking. Proteins, 55(2), 288–304. https://doi.org/https://doi.org/10.1002/prot.20035
- Yang, J. F., Wang, F., Chen, Y. Z., Hao, G. F., & Yang, G. F. (2019). LARMD: Integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. Briefings in Bioinformatics. bbz141. https://doi.org/https://doi.org/10.1093/bib/bbz141
- Zaretzki, J., Bergeron, C., Huang, T. W., Rydberg, P., Swamidass, S. J., & Breneman, C. M. (2013). RS-WebPredictor: A server for predicting CYP-mediated sites of metabolism on drug-like molecules. Bioinformatics (Oxford, England)), 29(4), 497–498. https://doi.org/https://doi.org/10.1093/bioinformatics/bts705
- Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors. Science, 368(6489), 409–412.
- Zhou, P., Yang, X.-L., Wang, X.-G., Hu, B., Zhang, L., Zhang, W., Si, H.-R., Zhu, Y., Li, B., Huang, C.-L., Chen, H.-D., Chen, J., Luo, Y., Guo, H., Jiang, R.-D., Liu, M.-Q., Chen, Y., Shen, X.-R., Wang, X., … Shi, Z.-L. (2020). A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579(7798), 270–273. https://doi.org/https://doi.org/10.1038/s41586-020-2012-7
- Ziebuhr, J., Snijder, E. J., & Gorbalenya, A. E. (2000). Virus-encoded proteinases and proteolytic processing in the Nidovirales. The Journal of General Virology, 81(Pt 4), 853–879. https://doi.org/https://doi.org/10.1099/0022-1317-81-4-853
- Zumla, A., Chan, J., Azhar, E., Hui, D., & Yuen, K. (2016). Coronaviruses – drug discovery and therapeutic options. Nature Reviews: Drug Discovery, 15(5), 327–347. https://doi.org/https://doi.org/10.1038/nrd.2015.37