PN 3

SimTech EXC 2075 Project Network 3 "Data-integrated model reduction for particles and continua"

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471 to 480 of 803 Results

README.md Mar 9, 2023 - Molecular simulation scripts for slit nanopores Markdown Text - 702 B - MD5: 6911101bd9e28fcef1923165b6ffbba7
runall.sh Mar 9, 2023 - Molecular simulation scripts for slit nanopores Shell Script - 548 B - MD5: 1361742c3203faab21d182abc9ad8d5e Bash script
runall.sh Mar 9, 2023 - Molecular simulation scripts for slit nanopores Shell Script - 548 B - MD5: 1361742c3203faab21d182abc9ad8d5e Bash script
tip4peps.itp Mar 9, 2023 - Molecular simulation scripts for slit nanopores application/vnd.shana.informed.formtemplate - 933 B - MD5: 1e996387ad050a7f9b8fbc84ae4abd4e GROMACS ff file
topol.top Mar 9, 2023 - Molecular simulation scripts for slit nanopores Unknown - 164 B - MD5: f630cf5c817b9271fa4fef71eb6831b1 GROMACS topology file
topol.top Mar 9, 2023 - Molecular simulation scripts for slit nanopores Unknown - 182 B - MD5: 372fdaff8d2edd874dce4f169a8f18bd GROMACS topology file
Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Mar 9, 2023 - PN 3-11 Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/DARUS-3373, DaRUS, V1 Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether...
45-ring_CG_resid39-152_cryoEM.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 44.8 MB - MD5: ece893fb0e4c783553ef62e82ca31fb2 simulations of ninjurin-1 rings in an apoptotic membrane (symmetric PS distribution among the leaflets) the ring contains 45 subunits ninjurin contains residues 39-152 in the cryoEM shape the dynamics of the pores is studied over 150mus coarse-grained simulation time using martini2.2P force field martini2.2P was chosen as our initial test as well...
45-ring_CG_resid79-152.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 30.9 MB - MD5: 198f9c7dfe0019557d4c4f05eed30837 control simulations of ninjurin-1 mutant rings in an apoptotic membrane (symmetric PS distribution among the leaflets) the ring contains 45 subunits ninjurin contains only the two transmembrane helices- i.e residues 79-152 the collapse of the pores is studied over 150mus coarse-grained simulation time using martini2.2P force field martini2.2P was...
charmm36-jul2017.ff.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 390.5 KB - MD5: 2465d1691943b03ccb7893d39f54fbdc charmm36m force field directory for GROMACS Please cite following papers if you use charmm36 parameters for protein: doi:10.1038/nmeth.4067 lipids: doi:10.1021/jp101759q cholesterol: doi:10.1021/jp207925m charmm-gui: doi:10.1002/jcc.20945 tip4p water: doi:10.1080/00268978500103111

README.md

Mar 9, 2023 - Molecular simulation scripts for slit nanopores

Markdown Text - 702 B -

runall.sh

Mar 9, 2023 - Molecular simulation scripts for slit nanopores

Shell Script - 548 B -

Bash script

runall.sh

Mar 9, 2023 - Molecular simulation scripts for slit nanopores

Shell Script - 548 B -

Bash script

tip4peps.itp

Mar 9, 2023 - Molecular simulation scripts for slit nanopores

application/vnd.shana.informed.formtemplate - 933 B -

GROMACS ff file

topol.top

Mar 9, 2023 - Molecular simulation scripts for slit nanopores

Unknown - 164 B -

GROMACS topology file

topol.top

Mar 9, 2023 - Molecular simulation scripts for slit nanopores

Unknown - 182 B -

GROMACS topology file

Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Mar 9, 2023 - PN 3-11

Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/DARUS-3373, DaRUS, V1

Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether...

45-ring_CG_resid39-152_cryoEM.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 44.8 MB -

simulations of ninjurin-1 rings in an apoptotic membrane (symmetric PS distribution among the leaflets) the ring contains 45 subunits ninjurin contains residues 39-152 in the cryoEM shape the dynamics of the pores is studied over 150mus coarse-grained simulation time using martini2.2P force field martini2.2P was chosen as our initial test as well...

45-ring_CG_resid79-152.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 30.9 MB -

control simulations of ninjurin-1 mutant rings in an apoptotic membrane (symmetric PS distribution among the leaflets) the ring contains 45 subunits ninjurin contains only the two transmembrane helices- i.e residues 79-152 the collapse of the pores is studied over 150mus coarse-grained simulation time using martini2.2P force field martini2.2P was...

charmm36-jul2017.ff.tar.gz

Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Gzip Archive - 390.5 KB -

charmm36m force field directory for GROMACS Please cite following papers if you use charmm36 parameters for protein: doi:10.1038/nmeth.4067 lipids: doi:10.1021/jp101759q cholesterol: doi:10.1021/jp207925m charmm-gui: doi:10.1002/jcc.20945 tip4p water: doi:10.1080/00268978500103111

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