SMMP v. 3.0-Simulating proteins and protein interactions in Python and Fortran

Computer Physics Communications

Volumn 178, Issue 6, 2008, Pages 459-470

  Meinke, Jan H ^a   Mohanty, Sandipan ^a   Eisenmenger, Frank ^b   Hansmann, Ulrich H E ^a,c  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

^b LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^c MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

FORTRAN package; Generalized ensemble simulations; Minimization; Monte Carlo; Protein folding; Python

Indexed keywords

COMPUTER SIMULATION; DISTRIBUTED COMPUTER SYSTEMS; GEOMETRY; MOLECULAR DYNAMICS; PARALLEL PROGRAMMING;

PROTEIN SIMULATION; STANDARD GEOMETRY MODEL;

PROTEINS;

EID: 39149110304     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2007.11.004     Document Type: Article

References (31)

1. Skolnick J., and Kolinski A. Annu. Rev. Phys. Chem. 40 (1989) 207
2. Scheraga H.A., Khalili M., and Liwo A. Annu. Rev. Phys. Chem. 58 (2007) 57
3. Pearlman D.A., et al. Comput. Phys. Comm. 91 (1995) 1
4. Brooks B.R., et al. J. Comp. Chem. 4 (1983) 187
5. Lindahl E., Hess B., and van der Spoel D. J. Mol. Model. 7 (2001) 306
6. Eisenmenger F., Hansmann U.H.E., Hayryan S., and Hu C.-K. Comput. Phys. Comm. 138 (2001) 192
7. Eisenmenger F., Hansmann U.H.E., Hayryan S., and Hu C.-K. Comput. Phys. Comm. 174 (2006) 422
8. Sippl M.J., Némthy G., and Scheraga H.A. J. Phys. Chem. 88 (1984) 6231
9. Nemethy G., et al. J. Phys. Chem. 96 (1992) 6472
10. Irbäck A. J. Phys.: Condens. Matter 17 (2005) S1553
11. Irbäck A., and Mohanty S. Biophys. J. 88 (2005) 1560
12. Favrin G., Irbäck A., and Sjunnesson F. J. Comp. Chem. 114 (2001) 8154
13. Message Passing Interface Forum, MPI: A Message-Passing Interface Standard (version 1.1), Technical report, 1995
14. Message Passing Interface Forum, MPI-2: Extensions to the Message Passing Interface, Technical report, 1997
15. Snir M., Otto S., Huss-Lederman S., Walker D., and Dongarra J. MPI-The Complete Reference vol. 1 (1998), The MIT Press
16. Gropp W., et al. MPI-The Complete Reference vol. 2 (1998), The MIT Press
17. Hukushima K., and Nemoto K. J. Phys. Soc. (Jap) 65 (1996) 1604
18. Geyer C.J., and Thompson E.A. J. Am. Stat. Assn. 90 (1995) 909
19. Hansmann U.H.E. Chem. Phys. Lett. 281 (1997) 140
20. Nadler W., and Hansmann U.H.E. Phys. Rev. E 75 (2007) 026109
21. Matsumoto M., and Nishimura T. ACM Trans. Model. Comput. Simul. 8 (1998) 3
22. G. van Rossum et al., Python Programming Language-Official Website
23. E. Jones, et al., SciPy: Open source scientific tools for Python, 2001
24. Masters C.L., et al. Proc. Natl. Acad. Sci. USA 82 (1985) 4245
25. Gordon D., Balbach J., Tycko R., and Meredith S. Biophys. J. 86 (2004) 428
26. Balbach J., et al. Biochemistry 39 (2000) 13748
27. Klimov D.K., and Thirumalai D. Structure 11 (2003) 295
28. Favrin G., Irbäck A., and Mohanty S. Biophys. J. 87 (2004) 3657
29. Gnanakaran S., Nussinov R., and Garcia A.E. J. Am. Chem. Soc. 128 (2006) 2158
30. Meinke J.H., and Hansmann U.H.E. J. Chem. Phys. 126 (2007) 014706
31. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, Palo Alto, CA, USA