GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics

Journal of Computational Chemistry

Volumn 30, Issue 12, 2009, Pages 1952-1958

  Allen, William J ^a   Lemkul, Justin A ^a   Bevan, David R ^a  

^a Fralin Life Science Institute   (United States)

Author keywords

Area per lipid headgroup; Lipid bilayer analysis; Lipid bilayer thickness; Molecular dynamics; Tessellation

Indexed keywords

ANALYSIS TOOLS; AREA PER LIPID HEADGROUP; CONTOUR PLOT; GRID-BASED; HEAD GROUPS; MEMBRANE THICKNESS; MOLECULAR DYNAMICS SIMULATIONS; SMALL MOLECULES; TESSELLATION; TWO-DIMENSIONAL;

DYNAMICS; MOLECULAR DYNAMICS;

LIPID BILAYERS;

DIPALMITOYLPHOSPHATIDYLCHOLINE; PEPTIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; LIPID BILAYER;

1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE; COMPUTER SIMULATION; LIPID BILAYERS; MODELS, MOLECULAR; PEPTIDES; SOFTWARE;

EID: 65549083717     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21172     Document Type: Article

References (25)

1. Klauda, J. B.; Kucerka, N.; Brooks, B. R.; Pastor, R. W.; Nagle, J. F. Biophys J 2006, 90, 2796.
2. Murtola, T.; Kupiainen, M.; Falck, E.; Vattulainen, I. J Chem Phys 2007, 126, 054707.
3. Shinoda, W.; Okazaki, S. J Chem Phys 1998, 109, 1517.
4. Sung, B. J.; Yethiraj, A. J Phys Chem B 2008, 112, 143.
5. Esteban-Martìn, S.; Salgado, J. Biophys J 2007, 93, 4278.
6. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J Comp Chem 2005, 26, 1701.
7. Periole, X.; Huber, T.; Marrink, S.-J.; Sakmar, T. P. J Am Chem Soc 2007, 129, 10126.
8. Tieleman, D. P.; MacCallum, J. L.; Ash, W. L.; Kandt, C.; Xu, Z.; Monticelli, L. J Phys Condens Matter 2006, 18, S1221.
9. Shepherd, C. M.; Vogel, H. J.; Tieleman, D. P. Biochem J 2003, 370, 233.
10. http://www.gnu.org/copyleft/gpl.html.
11. http://www.perl.com/.
12. Kandasamy, S. K.; Larson, R. G. Biophys J 2006, 90, 2326.
13. Case, D. A.; Cheatham, T.; Darden, T.; Gohlke, H.; Luo, R.; Merz, Jr., K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J Comp Chem 2005, 26, 1668.
14. Faraldo-Gûmez, J. D.; Smith, G. R.; Sansom, M. S. P. Eur Biophys J 2002, 31, 217.
15. Kandt, C.; Ash, W. L.; Tieleman, D. P. Methods 2007, 41, 475.
16. Berger, O.; Edholm, O.; Jhnig, F. Biophys J 1997, 72, 2002.
17. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J Chem Phys 1984, 81, 3684.
18. Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
19. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 103, 8577.
20. http://www.arc.vt.edu/arc/SystemX/index.php.
21. Tieleman, D. P.; Berendsen, H. J. C. J Chem Phys 1996, 105, 4871.
22. Nagle, J. F.; Tristam-Nagle, S. Biochem Biophys Acta 2000, 1469, 159.
23. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. J Comp Chem 2004, 25, 1605.
24. Tieleman, D. P.; Sansom, M. S. P.; Berendsen, H. J. C. Biophys J 1999, 76, 40.
25. http://www.matpack.de.