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22,461 to 22,470 of 25,353 Results

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
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 a...
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 c...
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
doublefil_CG_noDMP.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 4.8 MB - MD5: f73995912be7f84b7e0b939735a90abe ninjurin-1 double filaments coarse-grained simulations using Martini2 polarizable force field. the protein structure after simulation 1 was converted back to all-atom resolution of charmm36m force field using backward Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10...
doublefil_CG_withDMP.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 4.4 MB - MD5: ff1c621b0291dda0010f459c3721140c ninjurin-1 double filaments filled with dodecylmaltopyranoside coarse-grained simulations using Martini2 polarizable force field the protein structure after simulations was converted back to all-atom resolution of charmm36m force field using backward Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.100...
endlessmembranepatch_singlefilament_AA.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 23.2 MB - MD5: 7f4c6b23f12e1fdd5e1da6928146e460 here are two 1 µs-long all-atom simulations of ninjurin-1 (reisdues 39-152, cryoEM shape) single filaments attached to both sides of an endless membrane patch each filament comprises 5 ninjurin-1 subunits the system is periodic along the filament, i.e., along the z-axis
endlessmembranepatch_singlefilament_CG.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 14.3 MB - MD5: fcfbc234143822286b87b31ae761929f two 20 µs-long Martini2P simulations of ninjurin-1 (reisdues 39-152, cryoEM shape) single filaments attached to both sides of an endless membrane patch each filament comprises 10 ninjurin-1 subunits the system is periodic along the filament, i.e., along the z-axis Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/jo...

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

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 a...

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 c...

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

doublefil_CG_noDMP.tar.gz

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

Gzip Archive - 4.8 MB -

ninjurin-1 double filaments coarse-grained simulations using Martini2 polarizable force field. the protein structure after simulation 1 was converted back to all-atom resolution of charmm36m force field using backward Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.1000810 polarizable proteins: doi:10...

doublefil_CG_withDMP.tar.gz

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

Gzip Archive - 4.4 MB -

ninjurin-1 double filaments filled with dodecylmaltopyranoside coarse-grained simulations using Martini2 polarizable force field the protein structure after simulations was converted back to all-atom resolution of charmm36m force field using backward Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/journal.pcbi.100...

endlessmembranepatch_singlefilament_AA.tar.gz

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

Gzip Archive - 23.2 MB -

here are two 1 µs-long all-atom simulations of ninjurin-1 (reisdues 39-152, cryoEM shape) single filaments attached to both sides of an endless membrane patch each filament comprises 5 ninjurin-1 subunits the system is periodic along the filament, i.e., along the z-axis

endlessmembranepatch_singlefilament_CG.tar.gz

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

Gzip Archive - 14.3 MB -

two 20 µs-long Martini2P simulations of ninjurin-1 (reisdues 39-152, cryoEM shape) single filaments attached to both sides of an endless membrane patch each filament comprises 10 ninjurin-1 subunits the system is periodic along the filament, i.e., along the z-axis Please cite following papers if you use martini2.2p polarizable water: doi:10.1371/jo...

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