transition pathways between unliganded- and liganded- gp120 explored by adaptive parallel simulation and Markov state models

work flow

1. structures preparation: generating unliganded- and liganded- structure.
2. fixed-site MD simulation (gromacs).
3. Markov State Models (msmbuilder).
4. adaptive sampling (msmbuilder and python piptied).
5. Transition Path Theory
6. protein function analysis.

structures preparation

unliganded

4ZMJ

4ZMJ: remove gp41 and others (how to)

liganded

3JWD 2B4C 3FUS

3JWD_A: core N- C- 2B4C_G: core V3 liganded: core N- C- V3

fixed-site MD simulation

atomistic general MD simulation

fixed-sites

trajectory transform

MSMs required trajectories in .pdb file format.