Dynarepo 4ZRJ

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003FZ

Created: 11 Jul 2025
License: Apache License 2.0 (opens in a new tab)

Description

PPIs from test53, Classical MD simulations, 3 replicates of 500 ns

Molecular system

Starting structure: 4ZRJPDB 4ZRJ(opens in a new tab)
Force field: CHARMM36mTIP3P
Engine: GROMACS 2024.2
Method: Classical MD
Ensemble: NPT
Temperature: 310 K
Timestep: 2 fs
Composition: Molecules of interest
ProteinProtein · 2 chains6,453 atoms386 residues
Total6,453 atoms386 residues
Box dimensions: Dodecahedron
a10.13nm
b10.13nm
c7.171nm

Sequences

Sequence 1Protein · 302 residues

PKTFTVRIVT MDAEMEFNCE MKWKGKDLFD LVCRTLGLRE TWFFGLQYTI KDTVAWLKMD KKVLDHDVSK EEPVTFHFLA KFYPENAEEE LVQEITQHLF FLQVKKQILD EKIYCPPEAS VLLASYAVQA KYGDYDPSVH KRGFLAQEEL LPKRVINLYQ MTPEMWEERI TAWYAEHRGR ARDEAEMEYL KIAQDLEMYG VNYFAIRNKK GTELLLGVDA LGLHIYDPEN RLTPKISFPW NEIRNISYSD KEFTIKPLDK KIDVFKFNSS KLRVNKLILQ LCIGNHDLFM RRRKADSLEV QQ

Sequence 2Protein · 84 residues

TDMKRLDMEI EKEKVEYMEK SKHLQEQLNE LKTEIEALKL KERETALDIL HNENSDRGGS SKHNTIKKLT LQSWKSRVAF FEEL

Run	Outputs
replica 1	Trajectory Analyses
replica 2	Trajectory Analyses
replica 3	Trajectory Analyses

Files

67 files

All files

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Dynarepo 4ZRJ

Description

Molecular system

Sequences

Experiments

Files

Contributors

Acknowledgements