Refereed Papers of Dr. A. Bliznyuk:

1. A.A. Voityuk, A.A. Bliznyuk
   "Quantum chemical investigation of influence electronegativity of substituents on the reaction ability of Beta-chloroethylamine derivatives",
   Zh. Strukt. Khim., 1986, 27(3), p.25-29.
2. A.A. Bliznyuk, A.A. Voityuk
   "Complex programms MNDO-85 for calculations electronic structure, physicochemical indexes and reaction ability of molecules by MNDO, MNDOC and AM1",
   Zh. Strukt. Khim., 1986, 27(4), p.190-191.
3. A.A. Voityuk, A.A. Bliznyuk
   "MNDO calculations of systems with hydrogen bonds S-H",
   Zh. Strukt. Khim., 1987, 28(1), p.9-12.
4. A.A. Voityuk, A.A. Bliznyuk, K.Ya. Burshtein
   "Values of semiempirical parameters for atoms Br, I, Sn, Hg and Pb in MNDO method",
   Zh. Strukt. Khim., 1987, 28(1), p.13-17.
5. A.A. Bliznyuk, A.A. Voityuk
   "Programm for searching semiempirical parameters in MNDO methods",
   Zh. Strukt. Khim., 1987, 28(2), p.172-173.
6. A.A. Voityuk, A.A. Bliznyuk
   "MNDO calculations of systems with hydrogen bonds S-H",
   Theor. Chim. Acta, 1987, 71, p.327-331.
7. A.A. Voityuk, A.A. Bliznyuk
   "MNDO calculations of inorganic compounds of Sn",
   Zh. Neorg. Khim, 1987, 32, p.848-852.
8. A.A. Voityuk, A.A. Bliznyuk
   "Model quantum chemical investigation of the nature of the quadrupole Messbaur spectra in tris-Beta- diketonats Fe(III)",
   Koord. Khim, 1987, 13, p.1078-1081.
9. A.A. Voityuk, A.A. Bliznyuk
   "MNDO calculations of systems containing hydrogen bonds",
   Theor. Chim. Acta, 1987, 72, p.223-228.
10. A.A. Voityuk, A.A. Bliznyuk
    "Parameters MNDO methods for atom Zn",
    Zh. Strukt. Khim., 1987, 28(5), p.20-24.
11. A.A. Bliznyuk, A.A. Voityuk
    "MNDO/M calculations on hydrogen bonded systems",
    J. Mol. Struct. (Theochem), 1988, 164, p.343-349.
12. A.A. Bliznyuk, A.A. Voityuk
    "Calculations using MNDO/M, MNDO/H and AM1 of complexes with hydrogen bonds",
    Zh. Phys. Khim, 1988, 62, p.991-994.
13. A.A. Voityuk, A.A. Bliznyuk
    "Influence of nucleic bases protonation upon the energy of the Watson-Crick pairs",
    Molek. Biol., 1988, 22, p.1080-1086.
14. A.A. Bliznyuk, A.A. Voityuk
    "Investigation of the complexes with hydrogen bonds by the MNDO/M method",
    Zh. Strukt. Khim., 1988, 29(2), p.31-37.
15. A.A. Bliznyuk, A.A. Voityuk
    "MNDO parameters for atom Ca",
    Zh. Strukt. Khim., 1988, 29(5), p.156-157.
16. A.A. Voityuk, A.A. Bliznyuk
    "Quantum Chemical investigation of the effect of substutuents on the reactive ability of N-aril-N-(2-chloroethyl)amines",
    Zh. Organ. Khim., 1988, 24, p.152-157.
17. N.E. Fedotova, A.A. Voityuk, A.A. Bliznyuk, I.K. Igumenov
    "Thermochemical investigation of some Beta-diketonates of CU(II)",
    Koord. Khim., 1988, 14, p.1493-1506.
18. A.A. Voityuk, A.A. Bliznyuk, O.I. Lavrik
    "Transition state stabilization of aminoacyl-tRNA synthesases",
    Molek. Biol., 1989, 23, p.286-294.
19. A.A. Bliznyuk, A.A. Voityuk
    "Proton affinities of nucleic bases and their complexes",
    Zh. Phys. Khim., 1989, 63, p.1227-1230.
20. A.A. Voityuk, A.A. Bliznyuk
    "Estimation of the energy stabilization of the transition state due to hydrogen bonds",
    Kinetika and Katalis, 1989, 30, p.809-813.
21. A.A. Voityuk, A.A. Bliznyuk
    "Quantum mechanical study of the relative stability of protonated nucleic base pairs",
    Molek. Biol., 1989, 23, p.1107-1112.
22. A.A. Voityuk, A.A. Bliznyuk
    "Quantum Chemical study of mechanisms of hydrolysis of amids in the gas phase and in water",
    Izv. Acad. Nauk SSSR (ser. Khim), 1989, p.1785-1792.
23. A.A. Voityuk, A.A. Bliznyuk
    "The changes of stability of protein-nuclear complexes due to their interaction with water molecules. A quantum chemical study",
    Molek. Biol., 1989, 23, p.1289-1294.
24. A.A. Voityuk, A.A. Bliznyuk
    "Molecular orbital study of the relative stability of protonated nucleic acid base pairs",
    J. Mol. Struct. (Theochem), 1990, 205, p.119-128.
25. A.A. Voityuk, A.A. Bliznyuk
    "Molecular orbital study of the effect of water molecules on nucleic acid-protein interactions",
    J. Mol. Struct. (Theochem), 1990, 205, p.129-135.
26. A.A. Voityuk, A.A. Bliznyuk
    "Energy of Formation and structure of monoaquacomplexes of anions: results of MNDO/M calculations",
    Theor. and Eksper. Khim., 1990, p.66-70.
27. A.A. Voityuk, A.A. Bliznyuk
    "Quantum Chemical study of structure and properties of ammino-, aqua-, and hydroxo-complexes of Zn",
    Koord. Khim., 1990, 16, p.163-167.
28. A.A. Gall, S.O. Doronina, G.B. Shishkin, A.A. Voityuk, A.A. Bliznyuk
    "Diazabicycloalkanes with N atoms in knot positions. 17. Influence of substituents in benzo[b]-1,4-diazabicyclo[2.2.2] oktene on the proton affinities and open of the heterocycl by chlorocarbon ester",
    Khim. of Heterocyclic. Soed., 1989, p.366-371.
29. A.A. Bliznyuk, A.A. Voityuk, A.A. Sherbakov
    "Application of AM1 and PM3 methods for energy calculations and structure of O=PXYZ and S=PXYZ compounds",
    Zh. Strukt. Khim., 1990, 31(4), p.171-173.
30. A.A. Voityuk, A.A. Bliznyuk
    "Quantum Chemical study of mechanis of nucleophylic substitution to HCNO molecule",
    Theor. and Exsper. Khim., 1989, p.719-722.
31. A.A. Bliznyuk, M. Shen, H.F. Schaefer III
    "The dodecahedral N20 molecule. Some theoretical predictions",
    Chem. Phys. Lett., 1992, 198, p.249-252.
32. V.V. Vasiliev, A.A. Bliznyuk, A.A. Voityuk
    "A combined quantum chemical / molecular mechanical study of hydrogen bonded systems",
    Int. J. Quant. Chem., 1992, 44, p.897-930.
33. A.A. Voityuk, A.A. Bliznyuk
    "Quantum chemical investigation of ion-molecular complexes with hydrogen bonds",
    Zh. Strukt. Khim., 1992, 33(6), p.157-183.
34. A.A. Bliznyuk, H.F. Schaefer III, I.J. Amster
    "Proton affinities of lysine and histidine: A theoretical consideration of the discrepancy between experimantal results from the kinetic and bracketing methods",
    J. Am. Chem. Soc., 1993, 115, p.5149-5154.
35. A.A. Bliznyuk, J.E. Gready
    "A New Approach to Estimation of the Electrostatic Component of the Solvation Energy in Molecular Mechanics Calculations",
    J. Phys. Chem, 1995, 99, p.14506-14513.
36. A.A. Bliznyuk, J.E. Gready
    "Numerical Calculation of the Molecular Surface Area. I Assessment of Errors",
    J. Comp. Chem, 1996, 17(8), p.962-969.
37. A.A. Bliznyuk, J.E. Gready
    "Numerical Calculation of the Molecular Surface Area. II Speed of Calculation",
    J. Comp. Chem, 1996, 17(8), p.970-975.
38. A.A. Bliznyuk, J.E. Gready
    "Identification and Energetic Ranking of Possible Docking Sites for Pterin on Dihydrofolate Reductase",
    J. Comp.-Aided Mol. Des., 12(4):325-333, 1998
39. A. Rendell, A. Bliznyuk, T. Huber, A. Limae, J. Gready, S. Greatbanks, R. Schmidt
    "QM/MM studies of enzyme reaction mechanisms: building the computational engine",
    in HPC-Technology Driver for Academia, Business and Industry, Vol. 1, KY Lam BC Khoo, K Kumar, eds., Institute HPC, Singapore, 1998, pp.153-160.
40. A.A. Bliznyuk, J.E. Gready
    "Simple Method for Locating Possible Ligand Binding Sites on Protein Surfaces",
    J. Comp. Chem, 20(9):983-988, 1999
41. A.A. Bliznyuk, A.P. Rendell
    "Faster Gradients in Semiempirical Methods",
    J. Comp. Chem, 20(6):629-635, 1999
42. Titmuss SJ. Cummins PL. Bliznyuk AA. Rendell AP. Gready JE.
    "Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions",
    Chemical Physics Letters. 320(1-2):169-176, 2000
43. Allen TW., Bliznyuk A., Rendell AP., Kuyucak S., Chung SH.
    "The potassium channel: Structure, selectivity and diffusion",
    Journal of Chemical Physics. 112(18):8191-8204, 2000
44. H.A. Fruchtl, R.H. Nobes, A. Bliznyuk
    "Performance of Mopac on parallel computers",
    Journal of Molecular Structure (Theochem). 506:87-97, 2000
45. A.P. Rendell, A. Bliznyuk, T. Huber, R.H. Nobes, E.V. Akhmatskaya, H.A. Fruhtl, P.W.-C. Kung, V. Milman, H. Lung
    "Computational chemistry on Fujitsu vector-parallel processors: Dvelopment and performance of application software",
    Parallel Computing. 26(7-8):887-911, 2000
46. A.A. Bliznyuk, A.P. Rendell, T.W. Allen, S.H. Chung
    "The potassium ion channel: comparison of linear-scaling semiempirical and molecular mechanics representations of the electrostatic potential",
    Journal of Physical Chemistry B, 105(51):12673-12679, 2001
47. P.L. Cummins, S.J. Titmus, D. Jayatilaka, A.A. Bliznyuk, A.P. Rendell, J.E. Gready
    "Comparison of semiempirical and ab initio QM decomposition analyses for the interaction energy between molecules",
    Chemical Physics Letters, 352:245-251, 2002
48. S.J. Titmus, P.L. Cummins, A.P. Rendell, A.A. Bliznyuk, J.E. Gready
    "Comparison of linear-scaling semimepirical methods and combined quantum mechanical/molecular mechanical methods for enzyme reactions II: an energy decomposition analysis",
    Journal of Computational Chemistry, 23(14):1314-1322, 2002
49. J. Zuegg, A.A. Bliznyuk, J.E. Gready
    "Comparison of electrostatic potential around proteins calculated from Amber and AM1 charges: application to mutants of prion protein",
    Molecular Physics. 101(15):2437-2450, 2003
50. A.A. Bliznyuk and A.P. Rendell
    "Electronic effects in biomolecular simulations: Investigation of the KcsA potassium ion channel",
    Journal of Physical Chemistry B. 108(36):13866-13873, 2004
51. V. Vasilyev and A. Bliznyuk
    "Application of semiempirical quantum chemical methods as a scoring function in docking",
    Theoretical Chemistry Accounts. 112(4):313-317, 2004
52. H. Alonso, M.B. Gillies, P.L. Cummins, A.A. Bliznyuk, J.E. Gready
    "Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase",
    Journal of Computer-Aided Molecular Design. 19(3):165-187, 2005
53. H. Alonso, A.A. Bliznyuk, J.E. Gready
    "Combining docking and molecular dynamic simulations in drug design",
    Medicinal Research Reviews, 26(5):531-568, 2006

Book chapter: