Dataset Open Access

Equilibration simulations of TM domains of Bcl-2 proteins Mcl-1, Bok, and Bax

Javanainen, Matti

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 (15.3 MB)
Name Size
bax.cpt
md5:dbd5ddc08a82ad23c70dd04a7bf6b470
792.7 kB Download
bax.gro
md5:6c90b33ee4a213e4941bfaa70faceedb
2.3 MB Download
bax.ndx
md5:e54b6881b36e839d5cfe4e9a2d1b47e2
199.9 kB Download
bax.top
md5:5bd5fc2c4bfe5e2a4de1304029fabf44
250 Bytes Download
bax.tpr
md5:9535c348137a7aeb8baa6f8ba05a565b
1.2 MB Download
bok.cpt
md5:fa06469ce45203d5543932e2ce070f95
794.7 kB Download
bok.gro
md5:571ba5acfb40081ecbf59505e0efd497
2.3 MB Download
bok.ndx
md5:0b9a5c63136fe0b5791696cc6863b69e
200.4 kB Download
bok.top
md5:26e6f41276834670225cfae22428e19f
250 Bytes Download
bok.tpr
md5:e40e59f6f05292145a5065983a01bede
1.3 MB Download
bokf.tpr
md5:e40e59f6f05292145a5065983a01bede
1.3 MB Download
mcl1.cpt
md5:0baadcec8574cf8249f30049934651b5
790.6 kB Download
mcl1.gro
md5:4b577d0e6e1c485736bef7b81b48aba0
2.3 MB Download
mcl1.ndx
md5:650662f71a9142baa5128c9cdda7b4c7
199.4 kB Download
mcl1.top
md5:9c8907030f1ed16b20c09550e8042b96
253 Bytes Download
mcl1.tpr
md5:534efe9c483027b5e411478d31d5ed65
1.2 MB Download
md.mdp
md5:481e3e66d28c5b1b0bdf402975c4ef87
1.2 kB Download
TOP.tar
md5:da60dd6ed67e7bd8d0e410b1313fc20c
419.8 kB Download
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