4012224
doi
10.5281/zenodo.4012224
oai:zenodo.org:4012224
Equilibration simulations of TM domains of Bcl-2 proteins Mcl-1, Bok, and Bax
Javanainen, Matti
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
<p>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).</p>
<p>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.</p>
<p>[1] ADD</p>
Zenodo
2020-09-02
info:eu-repo/semantics/other
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