MemBuilder: A web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program

Bioinformatics

Volumn 30, Issue 3, 2014, Pages 439-441

  Ghahremanpour, Mohammad Mehdi ^a   Arab, Seyed Shahriar ^a,b   Aghazadeh, Saman Biook ^a,c   Zhang, Jin ^d,e   Van Der Spoel, David ^d  

^a INSTITUTE FOR RESEARCH IN FUNDAMENTAL SCIENCES IPM   (Iran)

^b TARBIAT MODARES UNIVERSITY   (Iran)

^c UNIVERSITY OF TEHRAN   (Iran)

^d UPPSALA UNIVERSITY   (Sweden)

^e ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CELL MEMBRANE; CHEMISTRY; COMPUTER GRAPHICS; COMPUTER PROGRAM; INTERNET; LIPID BILAYER; MOLECULAR DYNAMICS;

CELL MEMBRANE; COMPUTER GRAPHICS; INTERNET; LIPID BILAYERS; MODELS, BIOLOGICAL; MOLECULAR DYNAMICS SIMULATION; SOFTWARE;

EID: 84893232800     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt680     Document Type: Article

References (20)

1. Bond, P.J. and Sansom, M.S. (2006) Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc., 128, 2697-2704.
2. Chiu, S.W., et al. (2009) An improved united atom force field for simulation of mixed lipid bilayers. J. Phys. Chem. B, 113, 2748-2763.
3. Domanski, J., et al. (2010) Lipidbook: a public repository for force-field parameters used in membrane simulations. J. Membr. Biol., 236, 255-258.
4. Jambeck, J.P. and Lyubartsev, A.P. (2012a) Derivation and systematic validation of a refined all-atom force field for phosphatidylcholine lipids. J. Phys. Chem. B., 116, 3164-3179.
5. Jambeck, J.P. and Lyubartsev, A.P. (2012b) Another piece of the membrane puzzle: extending slipids further. J. Chem. Theor. Comput., 9, 774-784.
6. Jambeck, J.P. and Lyubartsev, A.P. (2012c) An extension and further validation of an all-atomistic force field for biological membranes. J. Chem. Theor. Comput., 8, 2938-2948.
7. Jo, S., et al. (2009) CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys. J., 97, 50-58.
8. Kandt, C., et al. (2007) Setting up and running molecular dynamics simulations of membrane proteins. Methods, 41, 475-488.
9. Oostenbrink, C., et al. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field.parameter sets 53A5 and 53A6. J. Comput. Chem., 25, 1656-1676.
10. Pandit, S.A., et al. (2008) Cholesterol packing around lipids with saturated and unsaturated chains: a simulation study. Langmuir, 24, 6858-6865.
11. Pronk, S., et al. (2013) GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics, 29, 845-854.
12. Rahmanpour, A., et al. (2012) Interaction of Piscidin-1 with zwitterionic versus anionic membranes: a comparative molecular dynamics study. J. Biomol. Struct. Dyn., 31, 1393-1403. DOI:10.1080/07391102.2012.737295.
13. Rothman, J.E. and Lenard, J. (1977) Membrane asymmetry. Science, 195, 743-753.
14. Spector, A.A. and Yorek, M.A. (1985) Membrane lipid composition and cellular function. J. Lipid Res., 26, 1015-1035.
15. Sprong, H., et al. (2001) How proteins move lipids and lipids move proteins. Nat. Rev. Mol. Cell Biol., 2, 504-513.
16. Tieleman, D.P., et al. (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim. Biophys. Acta, 1331, 235-270.
17. van Gunsteren, W.F., et al. (1996) Biomolecular Simulation: The {GROMOS96} Manual and User Guide. Zurich, Switzerland.
18. Wennberg, C.L., et al. (2012) Large influence of cholesterol on solute partitioning into lipid membranes. J. Am. Chem. Soc., 134, 5351-5361.
19. White, S.H. (2004) The progress of membrane protein structure determination. Protein Sci., 13, 1948-1949.
20. White, S.H., et al. (2001) How membranes shape protein structure. J. Biol. Chem., 276, 32395-32398.