Lipid Bilayers are home to membrane proteins,
accounting for 25-30% of the genome,
which carry out a variety of functions ranging from membrane trafficking and signal transduction to transportation of organic and inorganic compounds.
Therefore, accurate modeling of the lipid bilayers is very crucial in computational biology and chemistry.
Almost all membrane models are usually composed of only one type of phospholipids molecule that is quite far from the native biological state,
because biological membranes contain various types of lipids. Moreover, the asymmetry of lipid composition of the lipid bilayer is functionally important.
MemBuilder II prepares the initial configuration of a membrane model composed of different phospholipid molecules based on both united-atom and all-atom force fields and it is also dedicated to determine the lipid composition of each monolayer to support the asymmetry of the membrane bilayer.
Micelles are indispensable when working with integral membrane proteins.
They have become a powerful tool in the extraction of integral membrane proteins (IMPs) from biological membranes to study their structural and functional properties.
To complement the obtained in-vitro results, computational methods are being improved for in-silico study of IMPs structure and dynamic more accurately to understand how they interact with micelles.
In this regard, MemBuilder II is provided here to construct the initial structure of both homogenous and heterogeneous micelles based on the all-atom charmm-27 force field implemented in GROMACS software package helping us to study Micelle-IMPs interactions.
Liposomes are simple spherical enclosed structures with an aqueous interior, composed of curved lipid bilayers.
Liposomes have gained a variety applications including drug delivery since they were first described, particularly in pointing drugs toward tumor tissues selectively
Conventional anti-cancer drugs are small molecular weight chemicals, which affect non-specifically both healthy and tumor tissues leading to a therapy limiting cytotoxicity.
To decrease cytotoxicity, drugs can be encapsulated into small liposomes, which are capable to accumulate in tumors owning to the enhanced permeability and retention effect.
Consequently, MemBuilder II is dedicated to build liposome with different lipid compositions that can be useful for computational biologists and chemists to study Drug-Liposome interactions with an atomic resolution.