Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: Schemes and applications coupled to ab initio calculations

Journal of Physics Condensed Matter

Volumn 22, Issue 41, 2010, Pages

  Hagiwara, Yohsuke ^a   Tateno, Masaru ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO; AB INITIO CALCULATIONS; BIOLOGICAL MACROMOLECULE; BIOLOGICAL MOLECULE; COMPUTATIONAL COSTS; CRITICAL ISSUES; ELECTROSTATIC INTERACTIONS; FUNCTIONAL MECHANISMS; MACROMOLECULAR SYSTEMS; MOLECULAR MECHANICS CALCULATIONS; QM/MM CALCULATIONS; QUANTUM MECHANICAL; QUANTUM MECHANICS; REACTION CENTER;

CALCULATIONS; ELECTRONIC STRUCTURE; MOLECULAR MECHANICS; NUCLEIC ACIDS; QUANTUM THEORY;

MECHANISMS;

AMINO ACID TRANSFER RNA LIGASE; AZURIN;

CHEMISTRY; COMPUTER PROGRAM; MACROMOLECULE; METABOLISM; QUANTUM THEORY; REVIEW; THERMODYNAMICS;

AMINO ACYL-TRNA SYNTHETASES; AZURIN; MACROMOLECULAR SUBSTANCES; QUANTUM THEORY; SOFTWARE; THERMODYNAMICS;

EID: 78249277915     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/22/41/413101     Document Type: Article

References (57)

1. Merino E J, Boal A K and Barton J K 2008 Curr. Opin. Chem. Biol. 12 229
2. Jayapal P, SundararajanM, Hillier I H and Burton N A 2008 Phys. Chem. Chem. Phys. 10 4249
3. Kubar T and Elstner M 2008 J. Phys. Chem. B 112 8788
4. Ladik J, Bende A and Bogar F 2008 J. Chem. Phys. 128 105101
5. MacNaughton J B, Moewes A, Lee J S, Wettig S D, Kraatz H B, Ouyang L Z, Ching W Y and Kurmaev E Z 2006 J. Phys. Chem. B 110 15742
6. Hagiwara Y, Ohta T and Tateno M 2009 J. Phys.: Condens. Matter 21 064234
7. Ohta T, Hagiwara Y, Kang J, Nishikawa K, Yamamoto T, Nagao H and Tateno M 2010 J. Comput. Theor. Nanosci. 6 1
8. Mladenovic M, Fink R F, Thiel W, Schirmeister T and Engels B 2008 J. Am. Chem. Soc. 130 8696
9. Nakatani K, Dohno C, Ogawa A and Saito I 2002 Chem. Biol. 9 361
10. Solomon E I 2006 Inorg. Chem. 45 8012
11. Solt I, Simon I, Csaszar A G and Fuxreiter M 2007 J. Phys. Chem. B 111 6272
12. Vreven T and Morokuma K 2003 Theor. Chem. Acc. 109 125
13. Warshel A and Levitt M 1976 J. Mol. Biol. 103 227
14. Bruice T C and Kahn K 2000 Curr. Opin. Chem. Biol. 4 540
15. Field M J 2002 J. Comput. Chem. 23 48
16. Lin H and Truhlar D G 2007 Theor. Chem. Acc. 117 185
17. Mulholland A J 2005 Drug. Discov. Today 10 1393
18. Ryde U 2003 Curr. Opin. Chem. Biol. 7 136
19. Senn H M and Thiel W 2007 Curr. Opin. Chem. Biol. 11 182
20. Senn H M and Thiel W 2009 Angew. Chem. Int. Edn Engl. 48 1198
21. Gao J L, Ma S H, Major D T, Nam K, Pu J Z and Truhlar D G 2006 Chem. Rev. 106 3188
22. JorgensenW L 2007 J. Chem. Theory Comput. 3 1877
23. Warshel A, Kato M and Pisliakov A V 2007 J. Chem. Theory Comput. 3 2034
24. Hagiwara Y, Matsumura H and Tateno M 2009 J. Am. Chem. Soc. 131 16697
25. Matsumura H, Yamamoto T, Leow T C, Mori T, Salleh A B, Basri M, Inoue T, Kai T and Rahman R N 2008 Proteins 70 592
26. Lin H and Truhlar D G 2005 J. Phys. Chem. A 109 3991
27. Field M J, Albe M, Bret C, Proust-DeMartin F and Thomas A 2000 J. Comput. Chem. 21 1088
28. Reuter N, Dejaegere A, Maigret B and Karplus M 2000 J. Phys. Chem. A 104 1720
29. Amara P and Field M J 2003 Theor. Chem. Acc. 109 43
30. Eichinger M, Tavan P, Hutter J and Parrinello M 1999 J. Chem. Phys. 110 10452
31. Assfeld X and Rivail J L 1996 Chem. Phys. Lett. 263 100
32. Ferre N, Assfeld X and Rivail J L 2002 J. Comput. Chem. 23 610
33. Monard G, Loos M, Thery V, Baka K and Rivail J L 1996 Int. J. Quantum Chem. 58 153
34. Thery V, Rinaldi D, Rivail J L, Maigret B and Ferenczy G G 1994 J. Comput. Chem. 15 269
35. Amara P, Field M J, Alhambra C and Gao J L 2000 Theor. Chem. Acc. 104 336
36. Gao J L, Amara P, Alhambra C and Field M J 1998 J. Phys. Chem. A 102 4714
37. Pu J Z, Gao J L and Truhlar D G 2004 J. Phys. Chem. A 108 632
38. Walker R C, Crowley M F and Case D A 2008 J. Comput. Chem. 29 1019
39. Seabra G D, Walker R C, Elstner M, Case D A and Roitberg A E 2007 J. Phys. Chem. A 111 5655
40. Woodcock H L, Hodoscek M, Gilbert A T B, Gill P M W, Schaefer H F and Brooks B R 2007 J. Comput. Chem. 28 1485
41. Frisch M J et al 2003 Gaussian 03 (Pittsburgh, PA: Gaussian Inc)
42. Sherwood P et al 2003 J. Mol. Struct. (Theochem) 632 1
43. Harvey J N 2004 Faraday Discuss. 127 165
44. Torras J, Seabra G D M, Deumens E, Trickey S B and Roitberg A E 2008 J. Comput. Chem. 29 1564
45. Case D A, Cheatham T E, Darden T, Gohlke H, Luo R, Merz K M, Onufriev A, Simmerling C, Wang B and Woods R J 2005 J. Comput. Chem. 26 1668
46. Schmidt M W et al 1993 J. Comput. Chem. 14 1347
47. Holm R H, Kennepohl P K and Solomon E I 1996 Chem. Rev. 96 2239
48. Solomon E I, Szilagyi R K, DeBeer George S and Basumallick L 2004 Chem. Rev. 104 419
49. Nar H, Messerschmidt A, Huber R, van de Kamp M and Canters G W 1991 J. Mol. Biol. 221 765
50. George S D, Basumallick L, Szilagyi R K, Randall D W, Hill M G, Nersissian A M, Valentine J S, Hedman B, Hodgson K O and Solomon E I 2003 J. Am. Chem. Soc. 125 11314
51. Ibba M and Soll D 1999 Science 286 1893
52. Sankaranarayanan R and Moras D 2001 Acta Biochim. Pol. 48 323
53. Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S and Cusack S 2005 Nat. Struct. Mol. 12 923
54. Hagiwara Y, Nureki O and Tateno M 2009 FEBS Lett. 583 825
55. Hagiwara Y, Nureki O and Tateno M 2009 FEBS Lett. 583 1901
56. Hagiwara Y, Field M J, Nureki O and Tateno M 2010 J. Am. Chem. Soc. 132 2751
57. Ribas de Pouplana L and Schimmel P 2001 Trends. Biochem. Sci. 26 591