PN 3

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

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461 to 470 of 773 Results

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.pc...
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/...
resolution_conversion_5B.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 5.0 MB - MD5: 0a0c3474e575280bb3af6b5888ae2fc9 backwarding files for martini lipids containing 5 beads in the oleoyl chain to charmm36 force field please cite backward: doi:10.1021/ct400617g
singlefil_AA_resid39-152_alphafoldstructure.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 2.3 MB - MD5: 9dd0e348234886fd5780f1153d8f2060 this is a 1µs long AA simulation of a Ninj-1 (residues 39-152) single filament in water the single filament consists of 5 subunits each of the subunits has the structure that resulted from the alphafold prediction in the simulation the transmembrane helices 2 and 3 were position restraint to follow the reshaping of the rest of the protein.
singlefil_AA_resid39-152_cryoEMstructure.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 1.6 MB - MD5: c102e5587521a452aedef9a84cff0958 this is a 1µs long AA simulation of a Ninj-1 (residues 39-152) single filament in water the single filament consists of 5 subunits each of the subunits has the cryoEM structure in the simulation the transmembrane helices 2 and 3 were position restraint to follow the reshaping of the rest of the protein.
single_ninj_resid20-152_preapoptotic.tar.gz Mar 9, 2023 - Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Gzip Archive - 6.7 MB - MD5: 143570df7df2e927986cae3c6783e0d0 in these simulations the probability of membrane binding of ninjurin's N-terminus is investigated two membrane compositions are studied - the preapoptotic=asymmetric with PS present in the cytosolic leaflet only and apoptotic=symmetric, i.e. with PS symmetrically distributed between the two membrane leaflets the protein is anchored to the membran...
atomtypes.atp Mar 8, 2023 - Molecular simulation scripts for bulk solutions Unknown - 355 B - MD5: e1f3747cba280eb7f8128a90ece45689 GROMACS ff file
conf.gro Mar 8, 2023 - Molecular simulation scripts for bulk solutions Unknown - 349.2 KB - MD5: fe6d6c868091c51d3fe2b21fabaaa009 GROMACS configuration file
conf.gro Mar 8, 2023 - Molecular simulation scripts for bulk solutions Unknown - 347.0 KB - MD5: d73eb0b9b42daae86ace25c00d7b991d GROMACS configuration file

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.pc...

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/...

resolution_conversion_5B.tar.gz

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

Gzip Archive - 5.0 MB -

backwarding files for martini lipids containing 5 beads in the oleoyl chain to charmm36 force field please cite backward: doi:10.1021/ct400617g

singlefil_AA_resid39-152_alphafoldstructure.tar.gz

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

Gzip Archive - 2.3 MB -

this is a 1µs long AA simulation of a Ninj-1 (residues 39-152) single filament in water the single filament consists of 5 subunits each of the subunits has the structure that resulted from the alphafold prediction in the simulation the transmembrane helices 2 and 3 were position restraint to follow the reshaping of the rest of the protein.

singlefil_AA_resid39-152_cryoEMstructure.tar.gz

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

Gzip Archive - 1.6 MB -

this is a 1µs long AA simulation of a Ninj-1 (residues 39-152) single filament in water the single filament consists of 5 subunits each of the subunits has the cryoEM structure in the simulation the transmembrane helices 2 and 3 were position restraint to follow the reshaping of the rest of the protein.

single_ninj_resid20-152_preapoptotic.tar.gz

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

Gzip Archive - 6.7 MB -

in these simulations the probability of membrane binding of ninjurin's N-terminus is investigated two membrane compositions are studied - the preapoptotic=asymmetric with PS present in the cytosolic leaflet only and apoptotic=symmetric, i.e. with PS symmetrically distributed between the two membrane leaflets the protein is anchored to the membran...

atomtypes.atp

Mar 8, 2023 - Molecular simulation scripts for bulk solutions

Unknown - 355 B -

GROMACS ff file

conf.gro

Mar 8, 2023 - Molecular simulation scripts for bulk solutions

Unknown - 349.2 KB -

GROMACS configuration file

conf.gro

Mar 8, 2023 - Molecular simulation scripts for bulk solutions

Unknown - 347.0 KB -

GROMACS configuration file

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