All-atom-proteoliposome-preparation
This is the repository to our semi-automated strategy that has been developed in Peter Kasson Lab (Uppsala University) to facilitate atomistic proteoliposome preparation. The pipeline consists of bash/python scripts that are consecutively executed to (1) pre-process the input data at coarse-grained resolution (generated via the “Martini Maker” tool in CHARMM-GUI webserver) (2) insert viral fusion protein into a proteoliposome, (3) generate molecular topology, (4) perform energy minimization of a coarse-grained system, (5) perform system equilibration, (6) backmapp a coarse-grained system into atomistic resolution, (7) perform energy minimization of a backmapped system, (8) perform system equilibration. Our pipeline allows for a unified system preparation and is easily reproducible, and therefore can be customized according to individual project needs.
