NAMD goes quantum: An integrative suite for hybrid simulations

Nature Methods

Volumn 15, Issue 5, 2018, Pages 351-354

  Melo, Marcelo C R ^a,b   Bernardi, Rafael C ^a   Rudack, Till ^a,c   Scheurer, Maximilian ^d   Riplinger, Christoph ^e   Phillips, James C ^a   Maia, Julio D C ^f   Rocha, Gerd B ^f   Ribeiro, João V ^a   Stone, John E ^a   Neese, Frank ^g   Schulten, Klaus ^a,h   Luthey Schulten, Zaida ^a,b,h  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c RUHR UNIVERSITY BOCHUM   (Germany)

^d UNIVERSITY OF HEIDELBERG   (Germany)

^e FAccTs GmbH   (Germany)

^f FEDERAL UNIVERSITY OF PARAÍBA   (Brazil)

^g MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

^h University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE MONOPHOSPHATE DEAMINASE; ADENOSINE PHOSPHATE; AMINE; GLUTAMATE TRANSFER RNA LIGASE; HYDROXYL GROUP; TRANSFER RNA;

AMINOACYLATION; ANTICODON; ARTICLE; ATOM; BINDING SITE; CELL INTERACTION; CHEMICAL BOND; COVALENT BOND; DIPOLE; DISSOCIATION; EMBEDDING; ENERGY CONSERVATION; GENE EDITING; GENETIC CODE; HYBRID; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; QUANTUM CHEMISTRY; QUANTUM MECHANICS; REACTION ANALYSIS; SIMULATION; SOFTWARE; STATIC ELECTRICITY; THERMUS THERMOPHILUS; BIOLOGICAL MODEL; CHEMICAL MODEL; COMPUTER SIMULATION; QUANTUM THEORY;

COMPUTER SIMULATION; MODELS, BIOLOGICAL; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; QUANTUM THEORY; SOFTWARE; STATIC ELECTRICITY;

EID: 85046247663     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.4638     Document Type: Article

References (40)

1. Senn, H.M. & Thiel, W. Angew. Chem. Int. Edn Engl. 48, 1198-1229 (2009).
2. Field, M.J., Bash, P.A. & Karplus, M. J. Comput. Chem. 11, 700-733 (1990).
3. van der Kamp, M.W. & Mulholland, A.J. Biochemistry 52, 2708-2728 (2013).
4. Bernardi, R.C. & Pascutti, P.G. J. Chem. Theory Comput. 8, 2197-2203 (2012).
5. Retegan, M., Neese, F. & Pantazis, D.A. J. Chem. Theory Comput. 9, 3832-3842 (2013).
6. Coquelle, N. et al. Nat. Chem. 10, 31-37 (2018).
7. Lin, H. & Truhlar, D.G. Theor. Chem. Acc. 117, 185-199 (2007).
8. Jindal, G. & Warshel, A. J. Phys. Chem. B 120, 9913-9921 (2016).
9. Phillips, J.C. et al. J. Comput. Chem. 26, 1781-1802 (2005).
10. Jiang, W. et al. Comput. Phys. Commun. 185, 908-916 (2014).
11. Humphrey, W., Dalke, A. & Schulten, K. J. Mol. Graph. 14, 33-38 (1996).
12. Ribeiro, J.V. et al. Sci. Rep. 6, 26536 (2016).
13. Fu, H., Shao, X., Chipot, C. & Cai, W. J. Chem. Theory Comput. 12, 3506-3513 (2016).
14. Stewart, J.J. J. Comput. Aided Mol. Des. 4, 1-105 (1990).
15. Maia, J.D.C. et al. J. Chem. Theory Comput. 8, 3072-3081 (2012).
16. Neese, F. Wiley Interdiscip. Rev. Comput. Mol. Sci. 8, e1327 (2018).
17. Götz, A.W., Clark, M.A. & Walker, R.C. J. Comput. Chem. 35, 95-108 (2014).
18. Sethi, A., Eargle, J., Black, A.A. & Luthey-Schulten, Z. Proc. Natl. Acad. Sci. USA 106, 6620-6625 (2009).
19. Black Pyrkosz, A., Eargle, J., Sethi, A. & Luthey-Schulten, Z. J. Mol. Biol. 397, 1350-1371 (2010).
20. Pan, A.C., Sezer, D. & Roux, B. J. Phys. Chem. B 112, 3432-3440 (2008).
21. Riplinger, C., Pinski, P., Becker, U., Valeev, E.F. & Neese, F. J. Chem. Phys. 144, 024109 (2016).
22. Riccardi, D., Li, G. & Cui, Q. J. Phys. Chem. B 108, 6467-6478 (2004).
23. Warshel, A. & Levitt, M. J. Mol. Biol. 103, 227-249 (1976).
24. Darden, T., York, D. & Pedersen, L. J. Chem. Phys. 98, 10089-10092 (1993).
25. Stewart, J.J.P. J. Comput. Chem. 10, 209-220 (1989).
26. Stewart, J.J.P. J. Comput. Chem. 10, 221-264 (1989).
27. Sure, R. & Grimme, S. J. Comput. Chem. 34, 1672-1685 (2013).
28. Singh, U.C. & Kollman, P.A. J. Comput. Chem. 7, 718-730 (1986).
29. Walker, R.C., Crowley, M.F. & Case, D.A. J. Comput. Chem. 29, 1019-1031 (2008).
30. Lin, H. & Truhlar, D.G. J. Phys. Chem. A 109, 3991-4004 (2005).
31. Sherwood, P. et al. Faraday Discuss. 106, 79-92 (1997).
32. Frisch, M.J. et al. Gaussian 09, Revision A.02. (Gaussian, Inc., 2016).
33. Titov, A.V., Ufimtsev, I.S., Luehr, N. & Martinez, T.J. J. Chem. Theory Comput. 9, 213-221 (2013).
34. Shao, Y. et al. Mol. Phys. 113, 184-215 (2015).
35. Kulik, H.J., Zhang, J., Klinman, J.P. & Martínez, T.J. J. Phys. Chem. B 120, 11381-11394 (2016).
36. Sekine, S. et al. EMBO J. 22, 676-688 (2003).
37. Stewart, J.J.P. J. Mol. Model. 19, 1-32 (2013).
38. Best, R.B. et al. J. Chem. Theory Comput. 8, 3257-3273 (2012).
39. Dutra, J.D.L., Filho, M.A.M., Rocha, G.B., Simas, A.M. & Freire, R.O. PLoS One 10, e0124372 (2015).
40. Schoeler, C. et al. Nano Lett. 15, 7370-7376 (2015).