Dynarepo 2G45

Open

Omid Mokhtari;Hamed Khakzad;Yasaman Karami;

MD-A003NQ

Description

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

Starting structure: 2G45PDB 2G45(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 chains3,039 atoms193 residues
Total3,039 atoms193 residues
Box dimensions: Dodecahedron
a11.7nm
b11.7nm
c8.284nm

2

Sequence 1Protein · 117 residues

VRQVSKHAFS LKQLDNPARI PPCGWKXSKX DMRENLWLNL TDGSILXGRR YFDGSGGNNH AVEHYRETGY PLAVKLGTIT PDGADVYSYD EDDMVLDPSL AEHLSHFGID MLKMQKT

Sequence 2Protein · 76 residues

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

3

60 files

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DynaRepo Acknowledgements