Dynarepo 1OQE

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003NL

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: 1OQEPDB 1OQE(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 · 3 chains26,590 atoms1,681 residues
Total26,590 atoms1,681 residues
Box dimensions: Dodecahedron
a17.082nm
b17.082nm
c12.086nm

Sequences

3

Sequence 1Protein · 144 residues

VTQDCLQLIA DSETPTIQKG SYTFVPWLLS FKRGSALEEK ENKILVKETG YFFIYGQVLY TDKTYAMGHL IQRKKVHVFG DELSLVTLFR CIQNMPETLP NNSCYSAGIA KLEEGDELQL AIPRENAQIS LDGDVTFFGA LKLL

Sequence 2Protein · 31 residues

PTPCVPAECF DLLVRHCVAC GLLRTPRPKP A

Sequence 3Protein · 24 residues

PTPCVPAECF DLLVRHCVAC GLLR

Experiments

3

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

Files

500 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