References
- Ahmed, S. F., Quadeer, A. A., & McKay, M. R. (2020). Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses, 12(3), 254. https://doi.org/https://doi.org/10.3390/v12030254
- Becerra-Flores, M., & Cardozo, T. (2020). SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. International Journal of Clinical Practice, 74(8), e13525. https://doi.org/https://doi.org/10.1111/ijcp.13525
- Bilodeau, C. L., Lau, E. Y., Cramer, S. M., & Garde, S. (2019). Conformational Equilibria of Multimodal Chromatography Ligands in Water and Bound to Protein Surfaces. J Phys Chem B, 123(23), 4833–4843. https://doi.org/https://doi.org/10.1021/acs.jpcb.9b01218
- Brezovsky, J., Kozlikova, B., & Damborsky, J. (2018). Computational analysis of protein tunnels and channels. Methods in Molecular Biology (Clifton, N.J.).), 1685, 25–42. https://doi.org/https://doi.org/10.1007/978-1-4939-7366-8_3
- Buß, O., Rudat, J., & Ochsenreither, K. (2018). FoldX as protein engineering tool: better than random based approaches? Computational and Structural Biotechnology Journal, 16, 25–33. https://doi.org/https://doi.org/10.1016/j.csbj.2018.01.002
- Cao, X., Yin, R., Albrecht, H., Fan, D., & Tan, W. (2020). Cholesterol: A new game player accelerating vasculopathy caused by SARS-CoV-2? American Journal of Physiology. Endocrinology and Metabolism, 319(1), E197–e202. https://doi.org/https://doi.org/10.1152/ajpendo.00255.2020
- Chen, D. Y. (2020). SARS-CoV-2 desensitizes host cells to interferon through inhibition of the JAK-STAT pathway. bioRxiv,
- Chen, Y., & Qiu, F. (2020). Spike protein in the detection and treatment of novel coronavirus. Sheng wu yi Xue Gong Cheng Xue za Zhi = Journal of Biomedical Engineering = Shengwu Yixue Gongchengxue Zazhi, 37(2), 246–250. []. https://doi.org/https://doi.org/10.7507/1001-5515.202002050
- Chingin, K., & Barylyuk, K. (2018). Charge-state-dependent variation of signal intensity ratio between unbound protein and protein-ligand complex in electrospray ionization mass spectrometry: the role of solvent-accessible surface area. Analytical Chemistry, 90(9), 5521–5528. https://doi.org/https://doi.org/10.1021/acs.analchem.7b05349
- Cîrstea, A. E., Buzulică, R. L., Pirici, D., Ceauşu, M. C., Iman, R. V., Gheorghe, O. M., Neamţu, S. D., Stanca, L., Ene, R., Kumar-Singh, S., & Mogoantă, L. (2020). Histopathological findings in the advanced natural evolution of the SARS-CoV-2 infection. Rom J Morphol Embryol, 61(1), 209–218. https://doi.org/https://doi.org/10.47162/RJME.61.1.23
- Collier, G., Vellore, N. A., Latour, R. A., & Stuart, S. J. (2009). Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects. Biointerphases, 4(4), 57–64. https://doi.org/https://doi.org/10.1116/1.3266417
- Combs, S. A., Mueller, B. K., & Meiler, J. (2018). Holistic approach to partial covalent interactions in protein structure prediction and design with rosetta. Journal of Chemical Information and Modeling, 58(5), 1021–1036. https://doi.org/https://doi.org/10.1021/acs.jcim.7b00398
- David, T. I., Adelakun, N. S., Omotuyi, O. I., Metibemu, D. S., Ekun, O. E., Eniafe, G. O., Inyang, O. K., Adewumi, B., Enejoh, O. A., Owolabi, R. T., & Oribamise, E. I. (2018). Molecular docking analysis of phyto-constituents from Cannabis sativa with pfDHFR. Bioinformation, 14(9), 574–579. https://doi.org/https://doi.org/10.6026/97320630014574
- Dhanda, S. K., Mahajan, S., Paul, S., Yan, Z., Kim, H., Jespersen, M. C., Jurtz, V., Andreatta, M., Greenbaum, J. A., Marcatili, P., Sette, A., Nielsen, M., & Peters, B. (2019). IEDB-AR: Immune epitope database-analysis resource in 2019. Nucleic Acids Res, 47(W1), W502–w506. https://doi.org/https://doi.org/10.1093/nar/gkz452
- Eaaswarkhanth, M., Al Madhoun, A., & Al-Mulla, F. (2020). Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? International Journal of Infectious Diseases : IJID : official Publication of the International Society for Infectious Diseases, 96, 459–460. https://doi.org/https://doi.org/10.1016/j.ijid.2020.05.071
- Garcia, L., Bolleman, J., Gehant, S., Redaschi, N., & Martin, M., UniProt Consortium (2019). FAIR adoption, assessment and challenges at UniProt. Scientific Data, 6(1), 175. https://doi.org/https://doi.org/10.1038/s41597-019-0180-9
- Garg, V. K., Avashthi, H., Tiwari, A., Jain, P. A., Ramkete, P. W., Kayastha, A. M., & Singh, V. K. (2016). MFPPI - Multi FASTA ProtParam Interface. Bioinformation, 12(2), 74–77. https://doi.org/https://doi.org/10.6026/97320630012074
- Gerasimavicius, L., Liu, X., & Marsh, J. A. (2020). Identification of pathogenic missense mutations using protein stability predictors. Scientific Reports, 10(1), 15387. https://doi.org/https://doi.org/10.1038/s41598-020-72404-w
- Hildebrand, P. W., Rose, A. S., & Tiemann, J. K. S. (2019). Bringing molecular dynamics simulation data into view. Trends in Biochemical Sciences, 44(11), 902–913. https://doi.org/https://doi.org/10.1016/j.tibs.2019.06.004
- Koyama, T., Weeraratne, D., Snowdon, J. L., & Parida, L. (2020). Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment. Pathogens, 9(5), 324. https://doi.org/https://doi.org/10.3390/pathogens9050324
- Kurkcuoglu, Z., Koukos, P. I., Citro, N., Trellet, M. E., Rodrigues, J. P. G. L. M., Moreira, I. S., Roel-Touris, J., Melquiond, A. S. J., Geng, C., Schaarschmidt, J., Xue, L. C., Vangone, A., & Bonvin, A. M. J. J. (2018). Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J Comput Aided Mol Des , 32(1), 175–185. https://doi.org/https://doi.org/10.1007/s10822-017-0049-y
- Kutzner, C., Páll, S., Fechner, M., Esztermann, A., de Groot, B. L., & Grubmüller, H. (2019). More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry, 40(27), 2418–2431. https://doi.org/https://doi.org/10.1002/jcc.26011
- Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X. (2020). Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature, 581(7807), 215–220. https://doi.org/https://doi.org/10.1038/s41586-020-2180-5
- Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/https://doi.org/10.1021/ci200227u
- Liem, S. Y., & Popelier, P. L. A. (2019). The influence of water potential in simulation: A catabolite activator protein case study. Journal of Molecular Modeling, 25(8), 216 https://doi.org/https://doi.org/10.1007/s00894-019-4095-3
- Li, Z., Li, S., Wei, X., & Zhao, Q. (2019). Scaled Alternating Steepest Descent Algorithm Applied for Protein Structure Determination from Nuclear Magnetic Resonance Data. J Comput Biol, 26(9), 1020–1029. https://doi.org/https://doi.org/10.1089/cmb.2019.0013
- Li, J., Song, Y., Li, F., Zhang, H., & Liu, W. (2020). FWAVina: A novel optimization algorithm for protein-ligand docking based on the fireworks algorithm. Comput Biol Chem, 88, 107363 https://doi.org/https://doi.org/10.1016/j.compbiolchem.2020.107363
- Liu, Z. (2020). Identification of common deletions in the spike protein of SARS-CoV-2. J Virol,
- Lopes, J. L. S., Oliveira, D. C. A., Utescher, C. L. A., Quintilio, W., Tenório, E. C. N., Oliveira, C. L. P., Fantini, M. C. A., Rasmussen, M. K., Bordallo, H. N., Sant'Anna, O. A., & Botosso, V. F. (2019). Antigenic and physicochemical characterization of Hepatitis B surface protein under extreme temperature and pH conditions. Vaccine, 37(43), 6415–6425. https://doi.org/https://doi.org/10.1016/j.vaccine.2019.09.005
- Margraf, J. T., Hennemann, M., & Clark, T. (2020). EMPIRE: A highly parallel semiempirical molecular orbital program: 3: Born-Oppenheimer molecular dynamics. Journal of Molecular Modeling, 26(3), 43.https://doi.org/https://doi.org/10.1007/s00894-020-4293-z
- Miller, R. E., Tadmor, E. B., Gibson, J. S., Bernstein, N., & Pavia, F. (2016). Molecular dynamics at constant Cauchy stress. J Chem Phys, 144(18), 184107. https://doi.org/https://doi.org/10.1063/1.4948711
- Morse, J. S., Lalonde, T., Xu, S., & Liu, W. R. (2020). Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV. Chembiochem : a European Journal of Chemical Biology, 21(5), 730–738. https://doi.org/https://doi.org/10.1002/cbic.202000047
- Narang, S. S., Goyal, D., & Goyal, B. (2019). In silico-guided identification of potential inhibitors against β(2)m aggregation in dialysis-related amyloidosis. Journal of Biomolecular Structure and Dynamics. 1–15. https://doi.org/https://doi.org/10.1080/07391102.2019.1614093
- Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., Guo, L., Guo, R., Chen, T., Hu, J., Xiang, Z., Mu, Z., Chen, X., Chen, J., Hu, K., Jin, Q., Wang, J., & Qian, Z. (2020). Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nature Communications, 11(1), 1620. https://doi.org/https://doi.org/10.1038/s41467-020-15562-9
- Park, H., Lee, G. R., Kim, D. E., Anishchenko, I., Cong, Q., & Baker, D. (2019). High-accuracy refinement using Rosetta in CASP13. Proteins, 87(12), 1276–1282. https://doi.org/https://doi.org/10.1002/prot.25784
- Perkins, J. R., Diboun, I., Dessailly, B. H., Lees, J. G., & Orengo, C. (2010). Transient protein-protein interactions: Structural, functional, and network properties. Structure (London, England : 1993), 18(10), 1233–1243. https://doi.org/https://doi.org/10.1016/j.str.2010.08.007
- Rabaan, A. A., Al-Ahmed, S. H., Haque, S., Sah, R., Tiwari, R., Malik, Y. S., Dhama, K., Yatoo, M. I., Bonilla-Aldana, D. K., & Rodriguez-Morales, A. J. (2020). SARS-CoV-2, SARS-CoV, and MERS-COV: A comparative overview. Le Infezioni in Medicina, 28(2), 174–184.
- Sen, D. (2020). Identification of potential inhibitors of SARS-CoV-2 main protease and spike receptor from 10 important spices through structure-based virtual screening and molecular dynamic study. Journal of Biomolecular Structure and Dynamics, 1–22.
- Stourac, J., Vavra, O., Kokkonen, P., Filipovic, J., Pinto, G., Brezovsky, J., Damborsky, J., & Bednar, D. (2019). Caver Web 1.0: Identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Research, 47(W1), W414–w422. https://doi.org/https://doi.org/10.1093/nar/gkz378
- Strokach, A., Corbi-Verge, C., Teyra, J., & Kim, P. M. (2019). Predicting the effect of mutations on protein folding and protein-protein interactions. Methods in Molecular Biology (Clifton, N.J.).), 1851, 1–17. https://doi.org/https://doi.org/10.1007/978-1-4939-8736-8_1
- Vinayagam, S., & Sattu, K. (2020). SARS-CoV-2 and coagulation disorders in different organs. Life Sciences, 260, 118431.https://doi.org/https://doi.org/10.1016/j.lfs.2020.118431
- Walls, A. C., Park, Y.-J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell, 181(2), 281–292.e6. https://doi.org/https://doi.org/10.1016/j.cell.2020.02.058
- Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, N.Y.), 367(6483), 1260–1263. https://doi.org/https://doi.org/10.1126/science.abb2507
- Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science (New York, N.Y.).), 367(6485), 1444–1448. https://doi.org/https://doi.org/10.1126/science.abb2762
- Yang, M. (2020). NCBI's Conserved Domain Database and Tools for Protein Domain Analysis. Curr Protoc Bioinformatics, 69(1), e90.
- Zhang, D., Lazim, R., & Yip, Y. M. (2019). Incorporating polarizability of backbone hydrogen bonds improved folding of short α-helical peptides. Biophysical Journal, 117(11), 2079–2086. https://doi.org/https://doi.org/10.1016/j.bpj.2019.10.020
- Zhang, Y., & Sagui, C. (2015). Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI. Journal of Molecular Graphics & Modelling, 55, 72–84. https://doi.org/https://doi.org/10.1016/j.jmgm.2014.10.005