eBDIMS

eBDIMS is a coarse-grained hybrid Elastic Network/Brownian Dynamics model to generate transition pathways between two functional protein end-states.

An integrated tool to generate eBDIMS pathways is available at https://login.biophysics.kth.se/eBDIMS.

To fine-tune algorithm parameters, or to use large or incomplete structures, the stand-alone packages contained within this repository can be used.

Stand-alone packages

• pdbParser
• eBDIMS

Workflow for using stand-alone packages

1. Run the pdbParser script to retrieve the Carbon-alpha atoms for two end-state structures
2. The output files from step 1 (i.e. start and target end-state strucutres) are used as input to execute the eBDIMS simulation

References

• Orellana et al. Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations. Nature Communications 7, Article number: 12575 (2016). doi:10.1038/ncomms12575