Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes
نویسندگان
چکیده
منابع مشابه
Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes
The CELLmicrocosmos MembraneEditor (CmME) [1] enables researchers to generate PDB [2] based membrane structures in a convenient way. The lipid distribution is computed by algorithms working on the outer shapes of the molecules. For this reason, the computation and visualization process is very fast, while the atomistic structure of each single molecule remains unchanged. PDB membranes can be ex...
متن کاملCoarse-grained simulations of membranes under tension.
We investigate the properties of membranes under tension by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers. We give a comprising overview of the behavior of several membrane characteristics, such as the area per lipid, the monolayer overlap, the nematic order, and pressure profiles. Both the low-temperature regime, where the membranes are in a gel L(beta(')) phase,...
متن کاملCoarse-grained MD simulations of membrane protein-bilayer self-assembly.
Complete determination of a membrane protein structure requires knowledge of the protein position within the lipid bilayer. As the number of determined structures of membrane proteins increases so does the need for computational methods which predict their position in the lipid bilayer. Here we present a coarse-grained molecular dynamics approach to lipid bilayer self-assembly around membrane p...
متن کاملCoarse-grained protein-protein stiffnesses and dynamics from all-atom simulations.
Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamics simulations of one pair of units at a time. The computed relaxation times of this pair give a c...
متن کاملAll-atom and coarse-grained simulations of the forced unfolding pathways of the SNARE complex.
The SNARE complex, consisting of three proteins (VAMP2, syntaxin, and SNAP-25), is thought to drive membrane fusion by assembling into a four-helix bundle through a zippering process. In support of the above zippering model, a recent single-molecule optical tweezers experiment by Gao et al. revealed a sequential unzipping of SNARE along VAMP2 in the order of the linker domain → the C-terminal d...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Cheminformatics
سال: 2011
ISSN: 1758-2946
DOI: 10.1186/1758-2946-3-s1-p43