Dataset and analysis of molecular dynamics simulation of EpCAM ectodomain dimer.

ABSTRACT: The data provided and described here give insight into the solution dynamics of the dimer of human EpCAM ectodomain (EpEX). As the starting point, crystal structure of EpEX non-covalent dimer was used (PDB ID 4MZV). The coordinates of solvent-embedded dimer were used to generate a topology file, which was in turn used for all-atom molecular dynamics (MD) simulation run of 20 ns length using full-system periodic electrostatics at a constant temperature of 310 K and a constant pressure of 1 atm. The MD trajectory file (part of this dataset) contains 4000 frames corresponding to recording/sampling atom positions every 5 ps. The simulation run was then analyzed in terms of root mean square deviations (RMSD) of protein atoms, and non-covalent inter-subunit interactions. The MD trajectory and analyzed data enable-in contrast to the static crystal structure-detailed analysis of solution-like protein structural dynamics and support design of EpCAM-targetting binders and structure-based analysis of EpCAM interactome.

SUBMITTER: Pavsic M 

PROVIDER: S-EPMC8477132 | biostudies-literature |

REPOSITORIES: biostudies-literature