Dynarepo 4HDO

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003FY

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: 4HDOPDB 4HDO(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 chains7,846 atoms481 residues
Total7,846 atoms481 residues
Box dimensions: Dodecahedron
a11.445nm
b11.445nm
c8.096nm

Sequences

Sequence 1Protein · 314 residues

KPYEKVRIYR MDGSYRSVEL KHGNNTTVQQ IMEGMRLSQE TQQYFTIWIC SENLSLQLKP YHKPLQHVRD WPEILAELTN LDPQRETPQL FLRRDVRLPL EVEKQIEDPL AILILFDEAR YNLLKGFYTA PDAKLITLAS LLLQIVYGNY ESKKHKQGFL NEENLKSIVP VTKLKSKAPH WTNRILHEYK NLSTSEGVSK EMHHLQRMFL QNCWEIPTYG AAFFTGQIFT KASPSNHKVI PVYVGVNIKG LHLLNMETKA LLISLKYGCF MWQLGDTDTC FQIHSMENKM SFIVHTKQAG LVVKLLMKLN GQLM

Sequence 2Protein · 167 residues

MREYKLVVLG SGGVGKSALT VQFVQGIFVE KYDPTIEDSY RKQVEVDAQQ CMLEILDTAG TEQFTAMRDL YMKNGQGFAL VYSITAQSTF NDLQDLREQI LRVKDTDDVP MILVGNKCDL EDERVVGKEQ GQNLARQWNN CAFLESSAKS KINVNEIFYD LVRQINR

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

Files

69 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