PN 3

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

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481 to 490 of 803 Results

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:...
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...
Molecular simulation scripts for bulk solutions Mar 8, 2023 - NMR investigation of water confined by salt interface Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/DARUS-3179, DaRUS, V1 GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash script.
atomtypes.atp Mar 8, 2023 - Molecular simulation scripts for bulk solutions Unknown - 355 B - MD5: e1f3747cba280eb7f8128a90ece45689 GROMACS ff file

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:...

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...

Molecular simulation scripts for bulk solutions

Mar 8, 2023 - NMR investigation of water confined by salt interface

Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/DARUS-3179, DaRUS, V1

GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash script.

atomtypes.atp

Mar 8, 2023 - Molecular simulation scripts for bulk solutions

Unknown - 355 B -

GROMACS ff file

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