Dynarepo 2F4M

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003NP

Created: 29 Sept 2025
License: Apache License 2.0 (opens in a new tab)

Description

PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns

Molecular system

Starting structure: 2F4MPDB 2F4M(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 chains5,857 atoms356 residues
Total5,857 atoms356 residues
Box dimensions: Dodecahedron
a10.819nm
b10.819nm
c7.644nm

Sequences

2

Sequence 1Protein · 295 residues

GDSTILKVLQ SNIQHVQLYE NPVLQEKALT CIPVSELKRK AQEKLFRARK LDKGTNVSDE DFLLLELLHW FKEEFFRWVN NIVXSKXGGE TRSRDEALLP NDDELKWGAK NVENHYXDAX QLSNRFPRYN NPEKLLETRC GRCGEWANCF TLCCRALGFE ARYVWDYTDH VWTEVYSPSQ QRWLHCDACE DVCDKPLLYE IGWGKKLSYI IAFSKDEVVD VTWRYSCKHD EVMSRRTKVK EELLRETING LNKQRQLSLS ESRRKELLQR IIVELVEFIS PKTPRPGLEH HHHHH

Sequence 2Protein · 61 residues

GHPLEFLRNQ PQFQQMRQII QQNPSLLPAL LQQIGRENPQ LLQQISQHQE HFIQMLNEPV G

Experiments

3

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

Files

68 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

Contributors

Research groups: Delta team, Inria center at the University of Lorraine
Contact: yasaman.karami@inria.fr

Acknowledgements

DynaRepo Acknowledgements