Dynarepo 4M0W

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003FT

Created: 10 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: 4M0WPDB 4M0W(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 chains6,173 atoms393 residues
Total6,173 atoms393 residues
Box dimensions: Dodecahedron
a11.679nm
b11.679nm
c8.208nm

Sequences

Sequence 1Protein · 76 residues

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

Sequence 2Protein · 317 residues

VKTIKVFTTV DNTNLHTQLV DMSMTYGQQF GPTYLDGADV TKIKPHVNHE GKTFFVLPSD DTLRSEAFEY YHTLDESFLG RYMSALNHTK KWKFPQVGGL TSIKWADNNS YLSSVLLALQ QLEVKFNAPA LQEAYYRARA GDAANFCALI LAYSNKTVGE LGDVRETMTH LLQHANLESA KRVLNVVCKH CGQKTTTLTG VEAVMYMGTL SYDNLKTGVS IPCVCGRDAT QYLVQQESSF VMMSAPPAEY KLQQGTFLCA NEYTGNYQCG HYTHITAKET LYRIDGAHLT KMSEYKGPVT DVFYKETSYT TTIKPVS

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

Contributors

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

Acknowledgements

DynaRepo Acknowledgements