title: MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  To automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields, we provided MemBuilder as a web-based graphical user interface.
  
  
  METHODS
  MemBuilder is a free web server available from www.membuilder.org.
authors.affiliation: Department of Bioinformatics, School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran, School of Mathematics, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, Department of Computer Science, Faculty of Engineering, University of Tehran, Tehran, Iran, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden and Department of Chemistry, Zhejiang University, Hangzhou 310027, China.
authors.forename: Mohammad Mehdi
authors.initials: MM
authors.lastname: Ghahremanpour
authors.forename: Seyed Shahriar
authors.initials: SS
authors.lastname: Arab
authors.forename: Saman Biook
authors.initials: SB
authors.lastname: Aghazadeh
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.forename: David
authors.initials: D
authors.lastname: van der Spoel
mesh_terms: D002462:Cell Membrane / Q000737:chemistry; D003196:Computer Graphics; D020407:Internet; D008051:Lipid Bilayers / Q000737:chemistry*; D008954:Models, Biological; D056004:Molecular Dynamics Simulation; D012984:Software
chemical_list: D008051:Lipid Bilayers