Dynarepo 5J57

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003G0

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: 5J57PDB 5J57(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 chains6,031 atoms391 residues
Total6,031 atoms391 residues
Box dimensions: Dodecahedron
a11.729nm
b11.729nm
c8.283nm

Sequences

Sequence 1Protein · 264 residues

KQYPIINFTT AGATVQSYTN FIRAVRGRLT TGADVRHEIP VLPNRVGLPI NQRFILVELS NHAELSVTLA LDVTNAYVVG YRAGNSAYFF HPDNQEDAEA ITHLFTDVQN RYTFAFGGNY DRLEQLAGNL RENIELGNGP LEEAISALYY YSTGGTQLPT LARSFIICIQ MISEAARFQY IEGEMRTRIR YNRRSAPDPS VITLENSWGR LSTAIQESNQ GAFASPIQLQ RRNGSKFSVY DVSILIPIIA LMVYRCAPPP SSQF

Sequence 2Protein · 127 residues

VQLAETGGGL VEPGGSLRLS CAAPEFRLQY YTAGWFRQAP GKEREWVACI SAGGGVTYYT GSVQGRFTIS RDNAKRTVYL QMDSLKPEDT AVYSCAADLE YSQIMPSCRG SYGVRGQGTQ VTVSSAH

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

Files

62 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