References
- Nissen , P , Hansen , J , Ban , N , Moore , PB and Steitz , TA . 2000 . Science , 289 : 920
- Hansen , JL , Schmeing , TM , Moore , PB and Steitz , TA . 2002 . Proc. Natl. Acad. Sci. U.S.A. , 99 : 11670
- Bashan , A , Agmon , I , Zarivatch , R , Schluenzen , F , Harms , JM , Berisio , R , Bartels , H , Franceschi , F , Auerbach , T , Hansen , HA , Kossoy , E , Kessler , M and Yonath , A . 2003 . Mol. Cell , 11 : 91
- Ban , N , Nissen , P , Hansen , J , Moore , PB and Steitz , TA . 2000 . Science , 289 : 905
- Schmeing , TM , Huang , KS , Strobel , SA and Steitz , TA . 2005 . Nature , 438 : 520
- Schuwirth , BS , Borovinskaya , MA , Hau , CW , Zhang , W , Vila-Sanjurjo , A , Holton , JM and Cate , JH . 2005 . Science , 310 : 827
- Katunin , VI , Muth , GW , Strobel , SA , Wintermeyer , W and Rodnina , MV . 2002 . Mol. Cell , 10 : 339
- Sievers , A , Beringer , M , Rodnina , MV and Wolfenden , R . 2004 . Proc. Natl. Acad. Sci. U.S.A. , 101 : 7897
- Johansson , M , Bouakaz , E , Lovmar , M and Ehrenberg , M . 2008 . Mol. Cell 30 , 30 : 589
- Schroeder , GK and Wolfenden , R . 2007 . Biochemistry , 46 : 4037
- Thompson , J , Kim , DF , O'Connor , M , Lieberman , KR , Bayfield , MA , Gregory , ST , Green , R , Noller , HF and Dahlberg , AE . 2001 . Proc. Natl. Acad. Sci. U.S.A. , 98 : 9002
- Polacek , N , Gaynor , M , Yassin , A and Mankin , AS . 2001 . Nature , 411 : 498
- Beringer , M , Adio , S , Wintermeyer , W and Rodnina , M . 2003 . RNA , 9 : 919
- Trobro , S and Åqvist , J . 2005 . Proc. Natl. Acad. Sci. U.S.A. , 102 : 12395
- Gindulyte , A , Bashan , A , Agmon , I , Massa , L , Yonath , A and Karle , J . 2006 . Proc. Natl. Acad. Sci. U.S.A. , 103 : 13327
- Warshel , A . 1991 . Computer Modeling of Chemical Reactions in Enzymes and Solutions , New York : Wiley .
- Åqvist , J and Warshel , A . 1993 . Chem. Rev. , 93 : 2523
- Trobro , S and Åqvist , J . 2006 . Biochemistry , 45 : 7049
- Sharma , PK , Xiang , Y , Kato , M and Warshel , A . 2005 . Biochemistry , 44 : 11307
- Sanbonmatsu , KY , Joseph , S and Tung , CS . 2005 . Proc. Natl. Acad. Sci. U.S.A. , 102 : 15854
- Elstner , M , Porezag , D , Jungnickel , G , Elsner , J , Haugk , M , Frauenheim , T , Suhai , S and Seifert , G . 1998 . Phys. Rev. B , 58 : 7260
- Warshel , A and Karplus , M . 1972 . J. Am. Chem. Soc. , 94 : 5612
- Warshel , A and Levitt , M . 1976 . J. Mol. Biol. , 103 : 227
- Sherwood , P , de Vries , AH , Guest , MF , Schreckenbach , G , Catlow , CRA , French , SA , Sokol , AA , Bromley , ST , Thiel , W , Turner , AJ , Billeter , S , Terstegen , F , Thiel , S , Kendrick , J , Rogers , SC , Casci , J , Watson , M , King , F , Karlsen , E , Sjøvoll , M , Fahmi , A , Schäfer , A and Lennartz , C . 2003 . J. Mol. Struct. (THEOCHEM) , 632 : 1
- Senn , HM and Thiel , W . 2007 . Topics in Current Chemistry , Edited by: Reiher , M . Vol. 268 , 173 Berlin : Springer .
- Senn , HM and Thiel , W . 2007 . Curr. Op. Chem. Biol. , 11 : 182
- Lin , H and Truhlar , DG . 2007 . Theor. Chem. Acc. , 117 : 185
- Riccardi , D , Schaefer , P , Yang , Y , Yu , H , Ghosh , N , Prat-Resina , X , Knig , P , Li , G , Xu , D , Guo , H , Elstner , M and Cui , Q . 2006 . J. Phys. Chem. B , 110 : 6458
- MacKerell , AD Jr , Bashford , D , Bellott , RL , Dunbrack , RL Jr , Evanseck , JD , Field , MJ , Fischer , S , Gao , J , Guo , H , Ha , S , Joseph-McCarthy , D , Kuchnir , L , Kuczera , K , Lau , FTK , Mattos , C , Michnick , S , Ngo , T , Nguyen , DT , Prodhom , B , Reiher , WE III , Roux , B , Schlenkrich , M , Smith , JC , Stote , R , Straub , J , Watanabe , M , Wiorkiewicz-Kuczera , J , Yin , D and Karplus , M . 1998 . J. Phys. Chem. B , 102 : 3586
- MacKerell , AD Jr , Feig , M and Brooks , CL III . 2004 . J. Comput. Chem. , 25 : 1400
- Foloppe , N and MacKerell , AD Jr . 2000 . J. Comput. Chem. , 21 : 86
- MacKerell , AD Jr and Banavali , N . 2000 . J. Comput. Chem. , 21 : 105
- Dirac , PAM . 1929 . Proc. R. Soc. (London) A , 123 : 714
- Slater , JC . 1951 . Phys. Rev. , 81 : 385
- Vosko , SH , Wilk , L and Nusair , M . 1980 . Can. J. Phys. , 58 : 1200
- Becke , AD . 1988 . Phys. Rev. A , 38 : 3098
- Perdew , JP . 1986 . Phys. Rev. B , 33 : 8822
- Dunning , TH Jr . 1971 . J. Chem. Phys. , 55 : 716
- Chalmet , S , Harb , W and Ruiz-López , MF . 2001 . J. Phys. Chem. A , 105 : 11574
- Xu , D and Guo , H . 2009 . J. Am. Chem. Soc. , 131 : 9780
- Dunlap , BI , Connolly , JWD and Sabin , JR . 1979 . J. Chem. Phys. , 71 : 3396
- Eichkorn , K , Treutler , O , Öhm , H , Häser , M and Ahlrichs , R . 1995 . Chem. Phys. Lett. , 242 : 652
- Eichkorn , K , Weigend , F , Treutler , O and Ahlrichs , R . 1997 . Theor. Chem. Acc. , 97 : 119
- Guest , MF , Bush , IJ , van Dam , HJJ , Sherwood , P , Thomas , JMH , van Lenthe , JH , Havenith , RWA and Kendrick , J . 2005 . Mol. Phys. , 103 : 719
- GAMESS-UK is a package of ab initio programs. <http://www.cfs.dl.ac.uk/gamess-uk/index.shtml>
- ChemShell, a Computational Chemistry Shell. <www.chemshell.org>
- Tung , CS and Sanbonmatsu , KY . 2004 . Biophys. J. , 87 : 2714
- Schmeing , TM , Huang , KS , Kitchen , DE , Strobel , SA and Steitz , TA . 2005 . Mol. Cell , 20 : 437
- Jorgensen , WL , Chandrasekhar , J , Madura , JD , Impey , RW and Klein , ML . 1983 . J. Chem. Phys. , 79 : 926
- Nosé , S . 1984 . J. Chem. Phys. , 81 : 511
- Nosé , S . 1984 . Mol. Phys. , 52 : 255
- Hoover , WG . 1985 . Phys. Rev. A , 31 : 1695
- Martyna , GJ , Klein , ML and Tuckerman , M . 1992 . J. Chem. Phys. , 97 : 2635
- Jang , S and Voth , GA . 1997 . J. Chem. Phys. , 107 : 9514
- Schiferl , SK and Wallace , DC . 1985 . J. Chem. Phys. , 83 : 5203
- Kästner , J , Senn , HM , Thiel , S , Otte , N and Thiel , W . 2006 . J. Chem. Theor. Comput. , 2 : 452
- Liu , DC and Nocedal , J . 1989 . Math. Program. , 45 : 503
- Nocedal , J . 1980 . Math. Comp. , 35 : 773
- Billeter , SR , Turner , AJ and Thiel , W . 2000 . Phys. Chem. Chem. Phys. , 2 : 2177
- Kästner , J and Sherwood , P . 2008 . J. Chem. Phys. , 128 : 014106
- Henkelman , G and Jónsson , H . 1999 . J. Chem. Phys. , 111 : 7010
- Olsen , RA , Kroes , GJ , Henkelman , G , Arnaldsson , A and Jónsson , H . 2004 . J. Chem. Phys. , 121 : 9776
- Heyden , A , Bell , AT and Keil , FJ . 2005 . J. Chem. Phys. , 123 : 224101
- Henkelman , G , Uberuaga , BP and Jónsson , H . 2000 . J. Chem. Phys. , 113 : 9901
- Henkelman , G and Jónsson , H . 2000 . J. Chem. Phys. , 113 : 9978
- Jónsson , H , Mills , G and Jacobsen , KW . 1998 . in Classical and Quantum Dynamics in Condensed Phase Simulations , 385 London : World Scientific .
- Goumans , TPM , Catlow , CRA , Brown , WA , Kästner , J and Sherwood , P . 2009 . Phys. Chem. Chem. Phys. , 11 : 5431
- Kästner , J , Carr , JM , Keal , TW , Thiel , W , Wander , A and Sherwood , P . 2009 . J. Phys. Chem. A , 113 : 11856
- Bayly , CI , Cieplak , P , Cornell , W and Kollman , PA . 1993 . J. Phys. Chem. , 97 : 10269
- Torrie , GM and Valleau , JP . 1974 . Chem. Phys. Lett. , 28 : 578
- Torrie , GM and Valleau , JP . 1977 . J. Comput. Phys. , 23 : 187
- Kästner , J . 2009 . J. Chem. Phys. , 131 : 034109
- Kästner , J and Thiel , W . 2005 . J. Chem. Phys. , 123 : 144104
- Kästner , J and Thiel , W . 2006 . J. Chem. Phys. , 124 : 234106
- Humphrey , W , Dalke , A and Schulten , K . 1996 . J. Molec. Graph. , 14 : 33
- Jarzynski , C . 1997 . Phys. Rev. Lett. , 78 : 2690
- Senn , HM , O'Hagan , D and Thiel , W . 2005 . J. Am. Chem. Soc. , 127 : 13643
- el Saleh , SC and Potter , JD . 1985 . J. Biol. Chem. , 260 : 14775
- Qiao , GF , Li , BY , Zhou , YH , Lu , YJ and Schild , JH . 2009 . Int. J. Biol. Sci. , 5 : 293