Dynarepo 1KGY

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003NN

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: 1KGYPDB 1KGY(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 chains10,116 atoms638 residues
Total10,116 atoms638 residues
Box dimensions: Dodecahedron
a11.662nm
b11.662nm
c8.283nm

Sequences

2

Sequence 1Protein · 181 residues

AEETLMDSTT ATAELGWMVH PPSGWEEVSG YDENMNTIRT YQVCNVFESS QNNWLRTKFI RRRGAHRIHV EMKFSVRDCS SIPSVPGSCK ETFNLYYYEA DFDLATKTFP NWMENPWVKV DTIAADESFS QVDLGGRVMK INTEVRSFGP VSRNGFYLAF QDYGGCMSLI AVRVFYRKCP R

Sequence 2Protein · 138 residues

IVLEPIYWNS SNSKFLPGGG LVLYPQIGDK LDIICPKVDS KTVGQYEYYK VYMVDKDQAD RCTIKKENTP LLNCARPDQD VKFTIKFQEF SPNLWGLEFQ KNKDYYIIST SNGSLEGLDN QEGGVCQTRA MKILMKVG

Experiments

3

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

Files

140 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
structure.pdbPDB
trajectory.xtcXTC
clusters_00_screenshot_00.jpgJPG

Contributors

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

Acknowledgements

DynaRepo Acknowledgements