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

Mohammad Mehdi Ghahremanpour | Zendy; Seyed Shahriar Arab | Zendy; Saman Biook Aghazadeh | Zendy; Jin Zhang | Zendy; David van der Spoel | Zendy

Open Access

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

Author(s) -

Mohammad Mehdi Ghahremanpour,

Seyed Shahriar Arab,

Saman Biook Aghazadeh,

Jin Zhang,

David van der Spoel

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt680

Subject(s) - membrane , molecular dynamics , graphical user interface , computer science , lipid bilayer , interface (matter) , computational science , biological membrane , chemistry , molecule , chemical physics , biophysics , biological system , computational chemistry , biochemistry , biology , gibbs isotherm , organic chemistry , programming language

Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule. Moreover, the lipid composition and their distribution are functionally important. As a result, there is a necessity to prepare more realistic lipid membranes containing different types of lipids at physiological concentrations.

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