Equilibration simulations of TM domains of Bcl-2 proteins Mcl-1, Bok, and Bax
Creators
- 1. Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences
Description
Input files and final structures (after 1 microsecond) of simulations of Mcl-1, Bax, and Bok transmembrane domains (TMDs) in a POPC membrane. CHARMM36 parameters are used for lipids and proteins and the CHARMM-specific TIP3P model for water. The systems were set up using CHARMM-GUI, and simualted using GROMACS with the simulation parameters recommended for CHARMM (see md.mdp).
The simulations are described in detail in the paper [1]. Briefly, the final structures, given as .gro files here, were coarse-grained and used in high-throughput dimerization analyses. The dimer structures were clustered, and the most promising structures were fine-grained, and their stability was evaluated using atomistic simulations.
[1] ADD
Files
Files
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