10.5281/zenodo.4012224
https://zenodo.org/records/4012224
oai:zenodo.org:4012224
Javanainen, Matti
Matti
Javanainen
0000-0003-4858-364X
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences
Equilibration simulations of TM domains of Bcl-2 proteins Mcl-1, Bok, and Bax
Zenodo
2020
2020-09-02
10.5281/zenodo.4012223
Creative Commons Attribution 4.0 International
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