Abstract
A new approach to radical accelerate large-scale quantum chemical calculations of docking complexes, which require large computational times, is proposed. It takes into account the local nature of protein interaction with ligands and is based on a formation of special groups of atoms, which include the compactly located ligands and the protein atoms surrounding them. The procedure based on this approach allowed more than twice to reduce the time of a very resource-consuming calculation with respect to our previous high-speed semi-empirical method without a noticeable decrease in accuracy and provided a level of the time consumption appropriate for the large-scale serial calculations of such complexes.
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References
D. Mucs, R. A. Bryce, Expert Opin. Drug Discov., 2013, 8: 263.
O. Caldararu, M. A. Olsson, C. Riplinger, F. Neese, U. Ryde, J. Comput.-Aid. Molec. Design, 2017, 31: 87.
I. I. Baskin, V. A. Palyulin, N. S. Zefirov, Russ. Chem. Rev., 2009, 78: 495.
A. Cavalli, P. Carloni, M. Recanatini, Chem. Rev., 2006, 106: 3497.
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, N. S. Zefirov, Russ. Chem. Bull. (Int. Ed.), 2004, 53: 1335.
A. V. Sulimov, D. C. Kutov, E. V. Katkova, V. B. Sulimov, Adv. Bioinform., 2017, Article ID 7167691; DOI. org/10.1155/2017/7167691.
N. D. Yilmazer, M. Korth, Int. J. Molec. Sci., 2016, 17: 742.
K. M. Merz, Jr., Acc. Chem. Res., 2014, 47: 280.
P. Soderhjelm, J. Kongsted, S. Genheden, U. Ryde, Interdisciplin. Sci. Comput. Life Sci., 2010, 2: 21.
Y. Q. Jing, K. L. Han, Expert Opin. Drug Discov., 2010, 5: 33.
M. J. Phipps, T. Fox, C. S. Tautermann, C. K. Skylaris, J. Chem. Theory Comput., 2017, 13: 1837.
M. A. Olsson, P. Soderhjelm, U. Ryde, J. Comput. Chem., 2016, 37: 1589.
A. A. Adeniyi, M. E. S. Soliman, Drug Discovery Today, 2017, 22: 1216.
N. D. Yilmazer, M. Korth, Comput. Struct. Biotechnol. J., 2015, 13: 169.
A. Pecina, R. Meier, J. Fanfrlik, M. Lepsik, J. Rezac, P. Hobza, C. Baldauf, Chem. Comm., 2016, 52: 3312.
M. Lepsik, J. Rezac, M. Kolar, A. Pecina, P. Hobza, J. Fanfrlik, ChemPlusChem, 2013, 78: 921.
A. S. Christensen, T. Kubar, Q. Cui, M. Elstner, Chem. Rev., 2016, 116: 5301.
M. A. Olsson, P. Soderhjelm, U. J. Ryde, Comput. Chem., 2016, 37: 1589.
C. Barberot, J. C. Boisson, S. Gerard, H. Khartabil, E. Thiriot, G. Monard, E. Henon, Comput. Theor. Chem., 2014, 1028: 7.
J. J. P. Stewart, J. Mol. Model., 2013, 19: 1.
J. Hostas, J. Rezac, P. Hobza, Chem. Phys. Lett., 2013, 2–569: 161.
N. A. Anikin, A. S. Mendkovich, M. B. Kuzminskiy, A. M. Andreev, Russ. Chem. Bull. (Int. Ed.), 2008, 57: 428.
N. A. Anikin, A. M. Andreev, M. B. Kuz’minskii, A. S. Mendkovich, Russ. Chem. Bull. (Int. Ed.), 2008, 57: 1793.
H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, The Protein Data Bank. Nucleic Acids Res., 2000, 28: 235.
R. Wang, X. Fang, Y. Lu., S. Wang, J. Med. Chem., 2004, 47: 2977.
M. Elstner, Theor. Chim. Acta, 2006, 116: 316.
N. A. Anikin, V. L. Bugaenko, M. B. Kuz’minskii, A. S. Mendkovich, Russ. Chem. Bull. (Int. Ed.), 2014, 63: 346.
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Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1100–1103, June, 2018.
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Anikin, N.A., Andreev, A.M., Kuz’minskii, M.B. et al. A new approach for the acceleration of large-scale serial quantum chemical calculations of docking complexes. Russ Chem Bull 67, 1100–1103 (2018). https://doi.org/10.1007/s11172-018-2186-4
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DOI: https://doi.org/10.1007/s11172-018-2186-4