Dynarepo 4V0O

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003FU

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: 4V0OPDB 4V0O(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 chains7,453 atoms475 residues
Total7,453 atoms475 residues
Box dimensions: Dodecahedron
a11.037nm
b11.037nm
c7.805nm

Sequences

Sequence 1Protein · 309 residues

VRSVWLDAFN DPVAGISAYT PCVHTCNLFG DGENRLVIAD EDRKLKIWKG TQKASEHPLL DTPVAICSYP ALAVAAGSHI YIYRNLRPYY KFVLPPETVI TCMDVVKQAI DEPDAVSCLV VGTESGRILI LNPAGTAIVK NIWVGITPAM IAVQGELDVG YRITVAGRDG KLYHIRNGEL SQTIIQLEAQ PVGLVRLAKH VAVGCMNDVV HAYTPTGHKS WSLYLPCHIL AMQRMEVTGQ RNTKALIVAL SNGEVRVYNE KLLVSVHVSP NPVTALWFGR YGREDNTLLA ITKSGALDIK MLPRTANLE

Sequence 2Protein · 166 residues

SKKVNVLVVG LDNSGKTTII ERLKPRPRQA AEVAPTVGFT VDEVEKGPLT FTVFDMSGAG RYRTLWEQYY READAVVFVV DSADKLRMVV ARDEMEHMLK HSNMRKVPIL YFANKKDLPV AMPPVEIAQA LGLDDIKDRP WQIVPSNGLT GEGVDKGIDW LAERLS

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

Files

57 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