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with the fragment molecular orbital method. J Phys Chem 111:6904–6914
45. Klumpp K, Hang JQ, Rajendran S, Yang Y, Derosier A et al (2003) Two metal ion
mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV
RNase H inhibitors. Nucleic Acids Res 31:6852–6859
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Recent Advancements in Computing Reliable Binding Free Energies …
245
development. Wiley, Hoboken, NJ
28. Binda C, Wang J, Pisani L, Caccia C, Carotti A, Salvati P, Edmondson DE, Mattevi A (2007)
Structures of human monoamine oxidase B complexes with selective noncovalent inhibitors:
safinamide and coumarinanalogs. J Med Chem 50(23):5848–5852
29. De Colibus L, Li M, Binda C, Lustig A, Edmondson DE, Mattevi A (2005)
Three-dimensional structure of human monoamine oxidase A (MAO A): relation to the
structures of rat MAO A and human MAO B. Proc Natl Acad Sci 102(36):12684–12689
30. Ruddigkeit L, Van Deursen R, Blum LC, Reymond JL (2012) Enumeration of 166 billion
organic small molecules in the chemical universe database GDB-17. J Chem Inf Model 52
(11):2864–2875
31. Talele TT, Khedkar SA, Rigby AC (2010) Successful applications of computer aided drug
discovery: moving drugs from concept to the clinic. Curr Top Med Chem 10(1):127–141
32. Nam MH, Park M, Park H, Kim Y, Yoon S, Sawant VS, Choi JW, Park JH, Park KD, Min SJ,
Lee CJ (2017) Indole-substituted benzothiazoles and benzoxazoles as selective and reversible
MAO-B inhibitors for treatment of Parkinson’s disease. ACS Chem Neurosci 8(7):1519–1529
33. Balamurugan K, Murugan NA, Ågren H (2016) Multistep modeling strategy to improve the
binding affinity prediction of PET tracers to Ab42: case study with styrylbenzoxazole
derivatives. ACS Chem Neurosci 7(12):1698–1705
34. Murugan NA, Aidas K, Kongsted J, Rinkevicius Z, Agren H (2012) NMR spin-spin coupling
constants in polymethine dyes as polarity indicators. Chem Eur J 18:11677–11684
35. Murugan NA, Kongsted J, Rinkevicius Z, Agren H (2012) Color modeling of protein optical
probes. Phys Chem Chem Phys 14:1107–1112
36. Ryde U, Soderhjelm P (2016) Ligand-binding affinity estimates supported by
quantum-mechanical methods. Chem Rev 116:5520–5566
37. Cavalli A, Carloni P, Recanatini M (2006) Target-related applications of first principles
quantum chemical methods in drug design. Chem Rev 106:3497–3519
38. Nikitina E, Sulimov V, Zayets V, Zaitseva N (2004) Semiempirical calculations of binding
enthalpy for protein—ligand complexes. Int J Quantum Chem 97:747–763
39. Saen-oon S, Kuno M, Hannongbua S (2005) Binding energy analysis for wild-type and
Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: Quantum chemical calculations
based on the ONIOM method. Proteins Struct Funct Bioinf 61(4):859–869
40. Perakyla M, Pakkanen TA (1994) Quantum mechanical model assembly study on the
energetics of binding of arabinose, fucose, and galactose to L-arabinose-binding protein.
Proteins Struct Funct Genet 20:367–372
41. Perakyla M, Pakkanen TA (1995) Model assembly study of the ligand binding by
p-hydroxybenzoate hydroxylase: correlation between the calculated binding energies and the
experimental dissociation constants. Proteins Struct Funct Genet 21:22–29
42. Nikitina E, Sulimov V, Grigoriev F, Kondakova O, Luschekina S (2006) Mixed implicit/
explicit solvation models in quantum mechanical calculations of binding enthalpy for protein
—ligand complexes. Int J Quantum Chem 106:1943–1963
43. Liao RZ, Thiel W (2012) Comparison of QM-only and QM/MM models for the mechanism of
tungsten-dependent acetylene hydratase. J Chem Theory Comput 8(10):3793–3803
44. Fedorov DG, Kitaura K (2007) Extending the power of quantum chemistry to large systems
with the fragment molecular orbital method. J Phys Chem 111:6904–6914
45. Klumpp K, Hang JQ, Rajendran S, Yang Y, Derosier A et al (2003) Two metal ion
mechanism of RNA cleavage by HIV RNase H and mechanism-based design of selective HIV
RNase H inhibitors. Nucleic Acids Res 31:6852–6859
46. Budihas SR, Gorshkova I, Gaidamakov S, Wamiru A, Bona MK et al (2005) Selective
inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylatedtropolones. Nucleic Acids Res 33:1249–1256
47. Poongavanam V, Steinmann C, Kongsted J (2014) Inhibitor ranking through QM based
chelation calculations for virtual screening of HIV-1 RNase H inhibition. PLoS ONE 9(6):
e98659
Recent Advancements in Computing Reliable Binding Free Energies …
245