234
A. B. Rozhenko
methods, RI-DFT-based geometry optimization and RI-MP2 single-point energy
calculations can be combined for the model adducts of relatively large size. This
gives us believe to assert that, similarly to quantum chemistry of small molecules,
such kind of calculations will sooner or later turn into a routine.
Finally, the special event should be mentioned here as the scientific and public recognition of achievements of computational chemistry over the last decades
and its great prospects in the future: the Nobel Prize in Chemistry 2013 awarded
jointly to Martin Karplus, Michael Levitt and Arieh Warshel “for the development
of multiscale models for complex chemical systems”. Inter alia, the laureates laid
the foundation for the modern QM/MM approach [118] based nowadays on the ab
initio or DFT and MM/MD approaches. There is no doubt that the extent of the
DFT constituent will grow, increasing the reliability of the method by modeling
enzyme–inhibitor reactions.
References
1. Putz MV, Mingos DMP (eds) (2013) Applications of density functional theory to biological
and bioinorganic chemistry. Springer, Berlin. doi:10.1007/978-3-642-32750-6
2. Dahan A, Khamis M, Agbaria R, Karaman R (2012) Targeted prodrugs in oral drug delivery:
the modern molecular biopharmaceutical approach. Expert Opin Drug Del 9(8):1001–1013.
doi:10.1517/17425247.2012.697055
3. Kortagere S (ed) (2013) In silico models for drug discovery: methods in molecular biology,
vol 993. Humana Press, Totowa. doi:10.1007/978-1-62703-342-8
4. Jorgensen WL (2010) Drug discovery: pulled from a protein’s embrace. Nature 466(7302):42–
43. doi:10.1038/466042a
5. Sharma R (ed) (2012) Enzyme inhibition and bioapplications. InTech, Rijeka
6. Barril X (2012) Druggability predictions: methods, limitations, and applications. WIREs
Comput Mol Sci. doi:10.1002/wcms.1134. doi:10.1002/wcms.1134
7. Morris GM, Lim-Wilby M (2008) Molecular docking. In: Methods in molecular biology.
Spinger, Clifton, p 365–382
8. Puzyn T, Leszczynski J, Cronin MT (eds) (2010) Recent advances in QSAR studies, in series:
modern techniques and applications, vol 8. Springer, Netherlands. doi:10.1007/978-1-40209783-6
9. Utkov H, Livengood M, Cafiero M (2010) Using density functional theory methods for modeling induction and dispersion interactions in ligand–protein complexes. Ann Rep Comput
Chem 6:96–112. doi:10.1016/S1574-1400(10)06007-X
10. Zhang DW, Zhang JZH (2003) Molecular fractionation with conjugate caps for full quantum
mechanical calculation of protein–molecule interaction energy. J Chem Phys 119(7):3599–
3605. doi:10.1063/1.1591727
11. He X, Mei Y, Xiang Y, Zhang DW, Zhang JZH (2005) Quantum computational analysis for
drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins 61(2):423–432. doi:10.1002/prot.20578
12. York DM, Lee T-S (eds) (2009) Multi-scale quantum models for biocatalysis. In: Modern
techniques and applications, vol. 7, Springer, Dordrecht. doi:10.1007/978-1-4020-9956-4
13. Mulholland AJ (2007) Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions. Chem Cent J 1(1):19–24. doi:10.1186/1752-153X-1-19
14. Söderhjelm P, Aquilante F, Ryde U (2009) Calculation of protein–ligand interaction energies
by a fragmentation approach combining high-level quantum chemistry with classical manybody effects. J Phys Chem B 113(32):11085–11094
A. B. Rozhenko
methods, RI-DFT-based geometry optimization and RI-MP2 single-point energy
calculations can be combined for the model adducts of relatively large size. This
gives us believe to assert that, similarly to quantum chemistry of small molecules,
such kind of calculations will sooner or later turn into a routine.
Finally, the special event should be mentioned here as the scientific and public recognition of achievements of computational chemistry over the last decades
and its great prospects in the future: the Nobel Prize in Chemistry 2013 awarded
jointly to Martin Karplus, Michael Levitt and Arieh Warshel “for the development
of multiscale models for complex chemical systems”. Inter alia, the laureates laid
the foundation for the modern QM/MM approach [118] based nowadays on the ab
initio or DFT and MM/MD approaches. There is no doubt that the extent of the
DFT constituent will grow, increasing the reliability of the method by modeling
enzyme–inhibitor reactions.
References
1. Putz MV, Mingos DMP (eds) (2013) Applications of density functional theory to biological
and bioinorganic chemistry. Springer, Berlin. doi:10.1007/978-3-642-32750-6
2. Dahan A, Khamis M, Agbaria R, Karaman R (2012) Targeted prodrugs in oral drug delivery:
the modern molecular biopharmaceutical approach. Expert Opin Drug Del 9(8):1001–1013.
doi:10.1517/17425247.2012.697055
3. Kortagere S (ed) (2013) In silico models for drug discovery: methods in molecular biology,
vol 993. Humana Press, Totowa. doi:10.1007/978-1-62703-342-8
4. Jorgensen WL (2010) Drug discovery: pulled from a protein’s embrace. Nature 466(7302):42–
43. doi:10.1038/466042a
5. Sharma R (ed) (2012) Enzyme inhibition and bioapplications. InTech, Rijeka
6. Barril X (2012) Druggability predictions: methods, limitations, and applications. WIREs
Comput Mol Sci. doi:10.1002/wcms.1134. doi:10.1002/wcms.1134
7. Morris GM, Lim-Wilby M (2008) Molecular docking. In: Methods in molecular biology.
Spinger, Clifton, p 365–382
8. Puzyn T, Leszczynski J, Cronin MT (eds) (2010) Recent advances in QSAR studies, in series:
modern techniques and applications, vol 8. Springer, Netherlands. doi:10.1007/978-1-40209783-6
9. Utkov H, Livengood M, Cafiero M (2010) Using density functional theory methods for modeling induction and dispersion interactions in ligand–protein complexes. Ann Rep Comput
Chem 6:96–112. doi:10.1016/S1574-1400(10)06007-X
10. Zhang DW, Zhang JZH (2003) Molecular fractionation with conjugate caps for full quantum
mechanical calculation of protein–molecule interaction energy. J Chem Phys 119(7):3599–
3605. doi:10.1063/1.1591727
11. He X, Mei Y, Xiang Y, Zhang DW, Zhang JZH (2005) Quantum computational analysis for
drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. Proteins 61(2):423–432. doi:10.1002/prot.20578
12. York DM, Lee T-S (eds) (2009) Multi-scale quantum models for biocatalysis. In: Modern
techniques and applications, vol. 7, Springer, Dordrecht. doi:10.1007/978-1-4020-9956-4
13. Mulholland AJ (2007) Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions. Chem Cent J 1(1):19–24. doi:10.1186/1752-153X-1-19
14. Söderhjelm P, Aquilante F, Ryde U (2009) Calculation of protein–ligand interaction energies
by a fragmentation approach combining high-level quantum chemistry with classical manybody effects. J Phys Chem B 113(32):11085–11094