References
- Adams, J. M., & Cory, S. (1998). The Bcl-2 protein family: Arbiters of cell survival. Science, 281, 1322–1326. doi:10.1126/science.281.5381.132210.1126/science.281.5381.1322
- Allen, M. P., & Tildesley, D. J. (2003). Computer simulation of liquids. Oxford: Clarendon Press.
- Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., … Zardecki, C. (2002). The protein data bank. Acta Crystallographica. Section D, Biological Crystallography, 58, 899–907. doi:10.1107/S090744490200345110.1107/S0907444902003451
- Case, D. A., Darden, T. A., Cheatham, T. E., III, Simmerling, C. L., Wang, J., Duke, R. E., … Kollman, P. A. (2012). AMBER12. San Francisco, CA: University of California.
- Cieplak, P., Cornell, W. D., Bayly, C., & Kollman, P. A. (1995). Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. Journal of Computational Chemistry, 16, 1357–1377. doi:10.1002/jcc.54016110610.1002/(ISSN)1096-987X
- Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., … Kollman, P. A. (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 117, 5179–5197. doi:10.1021/Ja00124a00210.1021/ja00124a002
- Horn, A. H. C. (2014). Letter to the editor: Quercetin and taxifolin completely break MDM2-p53 association: Molecular dynamics simulation study by S. Verma, A. Singh, A. Mishra. Med Chem Res 2013, 22 (6) 2778–2787. Medicinal Chemistry Research, Epub ahead of print. doi:10.1007/s00044-014-1135-5
- Horn, A. H. C., & Kahler, A. (2013). The effect of fulvic acid on pre‐ and postaggregation state of Aβ17–42: Molecular dynamics simulation studies, S. Verma, A. Singh and A. Mishra, Biochim Biophys Acta 1834 (2013) 24–33. Biochimica et Biophysica Acta, 1834, 2867–2868. doi:10.1016/j.bbapap.2013.07.01210.1016/j.bbapap.2013.07.012
- Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins-Structure Function and Bioinformatics, 65, 712–725. doi:10.1002/Prot.2112310.1002/prot.v65:3
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14, 33–38. doi:10.1016/0263-7855(96)00018-510.1016/0263-7855(96)00018-5
- Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79, 926–935. doi:10.1063/1.44586910.1063/1.445869
- Ku, B., Liang, C., Jung, J. U., & Oh, B. H. (2011). Evidence that inhibition of BAX activation by BCL-2 involves its tight and preferential interaction with the BH3 domain of BAX. Cell Research, 21, 627–641. doi:10.1038/cr.2010.14910.1038/cr.2010.149
- Lee, S. B., Cha, K. H., Selenge, D., Solongo, A., & Nho, C. W. (2007). The chemopreventive effect of taxifolin is exerted through ARE-dependent gene regulation. Biological and Pharmaceutical Bulletin, 30, 1074–1079. doi:10.1248/bpb.30.1074
- Reed, J. C. (2002). Apoptosis-based therapies. Nature Reviews Drug Discovery, 1, 111–121. doi:10.1038/nrd72610.1038/nrd726
- Samuel, S., Tumilasci, V. F., Oliere, S., Nguyen, T. L., Shamy, A., Bell, J., & Hiscott, J. (2010). VSV oncolysis in combination with the BCL-2 inhibitor obatoclax overcomes apoptosis resistance in chronic lymphocytic leukemia. Molecular Therapy, 18, 2094–2103. doi:10.1038/mt.2010.18810.1038/mt.2010.188
- Seufi, A. M., Ibrahim, S. S., Elmaghraby, T. K., & Hafez, E. E. (2009). Preventive effect of the flavonoid, quercetin, on hepatic cancer in rats via oxidant/antioxidant activity: molecular and histological evidences. Journal of Experimental & Clinical Cancer Research, 28, 80. doi:10.1186/1756-9966-28-8010.1186/1756-9966-28-80
- Van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718. doi:10.1002/Jcc.2029110.1002/(ISSN)1096-987X
- Verma, S., Singh, A., & Mishra, A. (2014). Complex disruption effect of natural polyphenols on Bcl-2-Bax: Molecular dynamics simulation and essential dynamics study. Journal of Biomolecular Structure & Dynamics, 1–13, Epub ahead of print. doi: 10.1080/07391102.2014.931823