Molecular Dynamics Simulation of EpCAM Ectodomain Dimer

Published: 3 June 2021| Version 1 | DOI: 10.17632/44p89zc67y.1
Miha Pavšič


The dataset contains a molecular dynamics simulation of human EpCAM ectodomain (EpEX) dimer. As a starting point crystal structure of EpEX dimer was used (PDB ID 4MZV) to prepare a complete simulated system (structure PDB and topology PSF file) where the dimer was embedded in an electro-neutral water cube. After minimization, the simulation was run at a pressure of 1 atm and a temperature of 310 K for 20 ns with 2 fs timestep. For simulation, NAMD 2.11 was used. The resulting trajectory file (DCD format) was used to analyze frequency of inter-subunit contacts (Cytoscape network file, also supplied as PDF), and structure fluctuations (provided as list of per-residue Calpha RMSD values). The dataset also contains structure snapshots extracted from the trajectory (100 snapshots for subunits, and 100 for the dimer) corresponding to timepoints separated by 200 ps.



Univerza v Ljubljani Fakulteta za Kemijo in Kemijsko tehnologijo


Tumor Marker, Molecular Dynamics, Protein Dynamics, Protein Structure