Dynarepo 1UEX | MDRepo

Description

PPI from PDBbind, Classical MD simulations, 3 replicates of 500 ns

Molecular system

Starting structure: 1UEXPDB 1UEX(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 chains7,270 atoms450 residues
Total7,270 atoms450 residues
Box dimensions: Dodecahedron
a10.374nm
b10.374nm
c7.38nm

Sequences

Sequence 1Protein · 125 residues

GCLPDWSSYK GHCYKVFKKV GTWEDAEKFC VENSGHLASI DSKEEADFVT KLASQTLTKF VYDAWIGLRD ESKTQQCSPQ WTDGSSVVYE NVDEPTKCFG LDVHTEYRTW TDLPCGEKNP FICKS

Sequence 2Protein · 123 residues

GCLPDWSSYK GHCYKVFKVE KTWADAEKFC KELVNGGHLM SVNSREEGEF ISKLALEKMR IVLVWIGLSH FWRICPLRWT DGARLDYRAL SDEPICFVAE SFHNKWIQWT CNRKKSFVCK YRV

Sequence 3Protein · 202 residues

EPPLHDFYCS RLLDLVFLLD GSSRLSEAEF EVLKAFVVDM MERLRISQKW VRVAVVEYHD GSHAYIGLKD RKRPSELRRI ASQVKYAGSQ VASTSEVLKY TLFQIFSKID RPEASRIALL LMASQEPQRM SRNFVRYVQG LKKKKVIVIP VGIGPHANLK QIRLIEKQAP ENKAFVLSSV DELEQQRDEI VSYLCDLAPE AP

Experiments

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

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