Abstract
A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol−1.
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References
I. G. Tikhonova, I. I. Baskin, V. A. Palyulin, N. S. Zefirov, Izv. Akad. Nauk. Ser. Khim., 2004, 1282 [Russ. Chem. Bull., Int. Ed., 2004, 53, 1335].
J. H. Alzate-Morales, R. Contreras, A. Soriano, I. Tunon, E. Silla, Biophys. J., 2007, 92, 430.
T. Inaba, S. Tahara, N. Nisikawa, H. Kashiwagi, F. Sato, J. Comput. Chem., 2005, 26, 987.
D. N. Laikov, Yu. A. Ustynyuk, Izv. Akad. Nauk. Ser. Khim., 2005, 804 [Russ. Chem. Bull., Int. Ed., 2005, 54, 820].
A. Daniels, G. Scusseria, J. Chem. Phys., 1999, 110, 1321.
A. van der Vaart, D. Suarez, K. M. Merz, J. Chem. Phys., 2000, 113, 10512.
D. W. Zhang, J. Z. H. Zhang, J. Chem. Phys., 2003, 119, 3599.
D. W. Zhang, Y. Xiang, A. M. Gao, J. Z. H. Zhang, J. Chem. Phys., 2004, 120, 1145.
B. L. Grigorenko, A. V. Nemukhin, I. A. Topol, R. E. Cachau, S. K. Burt, Proteins: Structure, Function, and Bioinformatics, 2005, 60, 495.
Q. Cui, J. Chem. Phys., 2002, 117, 4720.
A. V. Nemukhin, B. L. Grigorenko, A. V. Rogov, I. A. Topol, S. K. Burt, Theor. Chem. Acc., 2004, 111, 36.
S. J. Titmus, P. L. Cummins, A. P. Rendell, A. A. Bliznyuk, J. E. Gready, J. Comput. Chem., 2002, 23, 1314.
T. Kruger, M. Elstner, P. Schiffels, T. Frauenheim, J. Chem. Phys., 2005, 122, 114110.
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 Research, 2000, 28, 235.
R. Wang, Y. Lu, X. Fang, S. Wang, J. Chem. Inf. Comput. Sci., 2004, 44, 2114.
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Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.
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Anikin, N.A., Mendkovich, A.S., Kuzminskiy, M.B. et al. A method and program for mass quantum chemical calculations of protein—ligand docking complexes. Russ Chem Bull 57, 428–430 (2008). https://doi.org/10.1007/s11172-008-0067-y
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DOI: https://doi.org/10.1007/s11172-008-0067-y