360
T. Miyakawa et al.
2. Downward J (2003) Nat Rev Cancer 3:11–22
3. Goodsell DS (1999) Oncologist 4:263–264
4. Pai EF, Krengel U, Petsko GA, Goody RS, Kabsch W, Wittinghofer A (1990) EMBO J
9:2351–2359
5. Milburn MV, Tong L, deVos AM, Brünger A, Yamaizumi Z, Nishimura S, Kim SH (1990)
Science 247:939–945
6. Coleman DE, Berghuis AM, Lee E, Linder ME, Gilman AG, Sprang SR (1994) Science
265:1405–1412
7. Frech M, Darden TA, Pedersen LG, Foley CK, Charifson PS, Anderson MW, Wittinghofer A
(1994) Biochemistry 33:3237–3244
8. Glennon TM, Villa J, Warshel A (2000) Biochemistry 39:9641–9651
9. Langen R, Shweins T, Warshel A (1992) Biochemistry 31:8691–8696
10. Privé GG, Milburn MV, Tong L, de Vos AM, Yamaizumi Z, Nishimura S, Kim SH (1992)
Proc Natl Acad Sci USA 89:3649–3653
11. Schweins T, Geyer M, Scheffzek K, Warshel A, Kalbitzer HR, Wittinghofer A (1995) Nat
Struct Biol 2:36–44
12. Schweins T, Warshel A (1996) Biochemistry 35:14232–14243
13. Maegley KA, Admiraal SJ, Herschlag D (1996) Proc Natl Acad Sci USA 93:8160–8166
14. Admiraal SJ, Herschlag D (1995) Chem Biol 2:729–739
15. Herschlag D, Jencks WP (1989) J Am Chem Soc 111:7587–7596
16. Skoog MT, Jencks WP (1984) J Am Chem Soc 106:7597–7606
17. Allin C, Armadian MR, Wittinghofer A, Gerwert K (2001) Proc Natl Acad Sci USA 98:7754–
7759
18. Allin C, Gerwert K (2001) Biochemistry 40:3037–3046
19. Cepus V, Scheidig AJ, Goody RS, Gerwert K (2001) Biochemistry 37:10263–10271
20. Du X, Frei H, Kim SH (2000) J Biol Chem 275:8492–8500
21. Wang JH, Xiao DG, Deng H, Webb MR, Callender R (1998) Biochemistry 37:11106–11116
22. Zhu G, Liu J, Terzyan S, Zai P, Li G, Zhang XC (2003) J Biol Chem 278:2452–2460
23. Cheng H, Sukal S, Deng H, Leyh TS, Callender R (2001) Biochemistry 40:4035–4043
24. Herschlag D, Jencks WP (1986) J Am Chem Soc 108:7938–7946
25. Foley CL, Pedersen LG, Charifson PS, Darden TA, Wittinghofer A, Pai EF, Andersen MW
(1992) Biochemistry 31:4951–4959
26. Worth GA, Edge C, Richards WG (1995) J Mol Model 1:123–142
27. Mello LV, van Aalten DMF, Findlay JBC (1997) Protein Eng 10:381–387
28. Futatsugi N, Tsuda M (2001) Biophys J 81:3483–3488
29. Kobayashi C, Saito S (2010) Biophys J 99:3726–3734
30. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong W, Zhang G, Yang R, Cieplak P, Luo R, Lee
T, Caldwell J, Wang J, Kollman P (2003) J Comput Chem 24:1999–2012
31. Miyakawa T, Morikawa R, Takasu M, Sugimori K, Kawaguchi K, Saito H, Nagao H (2012)
Prog Theory Chem Phys 26:525–543
32. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys
79:926–935
33. Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327–341
34. Adelman SA, Doll JD (1976) J Chem Phys 64:2375–2388
35. Grest GS, Kremer K (1986) Phys Rev A 33:3628–3631
36. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) J Chem Phys
81:3684–3690
T. Miyakawa et al.
2. Downward J (2003) Nat Rev Cancer 3:11–22
3. Goodsell DS (1999) Oncologist 4:263–264
4. Pai EF, Krengel U, Petsko GA, Goody RS, Kabsch W, Wittinghofer A (1990) EMBO J
9:2351–2359
5. Milburn MV, Tong L, deVos AM, Brünger A, Yamaizumi Z, Nishimura S, Kim SH (1990)
Science 247:939–945
6. Coleman DE, Berghuis AM, Lee E, Linder ME, Gilman AG, Sprang SR (1994) Science
265:1405–1412
7. Frech M, Darden TA, Pedersen LG, Foley CK, Charifson PS, Anderson MW, Wittinghofer A
(1994) Biochemistry 33:3237–3244
8. Glennon TM, Villa J, Warshel A (2000) Biochemistry 39:9641–9651
9. Langen R, Shweins T, Warshel A (1992) Biochemistry 31:8691–8696
10. Privé GG, Milburn MV, Tong L, de Vos AM, Yamaizumi Z, Nishimura S, Kim SH (1992)
Proc Natl Acad Sci USA 89:3649–3653
11. Schweins T, Geyer M, Scheffzek K, Warshel A, Kalbitzer HR, Wittinghofer A (1995) Nat
Struct Biol 2:36–44
12. Schweins T, Warshel A (1996) Biochemistry 35:14232–14243
13. Maegley KA, Admiraal SJ, Herschlag D (1996) Proc Natl Acad Sci USA 93:8160–8166
14. Admiraal SJ, Herschlag D (1995) Chem Biol 2:729–739
15. Herschlag D, Jencks WP (1989) J Am Chem Soc 111:7587–7596
16. Skoog MT, Jencks WP (1984) J Am Chem Soc 106:7597–7606
17. Allin C, Armadian MR, Wittinghofer A, Gerwert K (2001) Proc Natl Acad Sci USA 98:7754–
7759
18. Allin C, Gerwert K (2001) Biochemistry 40:3037–3046
19. Cepus V, Scheidig AJ, Goody RS, Gerwert K (2001) Biochemistry 37:10263–10271
20. Du X, Frei H, Kim SH (2000) J Biol Chem 275:8492–8500
21. Wang JH, Xiao DG, Deng H, Webb MR, Callender R (1998) Biochemistry 37:11106–11116
22. Zhu G, Liu J, Terzyan S, Zai P, Li G, Zhang XC (2003) J Biol Chem 278:2452–2460
23. Cheng H, Sukal S, Deng H, Leyh TS, Callender R (2001) Biochemistry 40:4035–4043
24. Herschlag D, Jencks WP (1986) J Am Chem Soc 108:7938–7946
25. Foley CL, Pedersen LG, Charifson PS, Darden TA, Wittinghofer A, Pai EF, Andersen MW
(1992) Biochemistry 31:4951–4959
26. Worth GA, Edge C, Richards WG (1995) J Mol Model 1:123–142
27. Mello LV, van Aalten DMF, Findlay JBC (1997) Protein Eng 10:381–387
28. Futatsugi N, Tsuda M (2001) Biophys J 81:3483–3488
29. Kobayashi C, Saito S (2010) Biophys J 99:3726–3734
30. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong W, Zhang G, Yang R, Cieplak P, Luo R, Lee
T, Caldwell J, Wang J, Kollman P (2003) J Comput Chem 24:1999–2012
31. Miyakawa T, Morikawa R, Takasu M, Sugimori K, Kawaguchi K, Saito H, Nagao H (2012)
Prog Theory Chem Phys 26:525–543
32. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys
79:926–935
33. Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327–341
34. Adelman SA, Doll JD (1976) J Chem Phys 64:2375–2388
35. Grest GS, Kremer K (1986) Phys Rev A 33:3628–3631
36. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) J Chem Phys
81:3684–3690