Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems
This repo provides all details to repertory and validate the paper Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems (doi: https://doi.org/10.1101/2020.04.27.062539)
- Preparation folder contains topology, .mdp and .gro file to generate .tpr files to perform simulation with TIP4P-Ew water model
- TIP3P-MD1 and MD2 contains plumed.dat files to monitor and .tpr files to run MD simulations. MD1 and MD2 denotes MD simulations starting with different initial starting velocities.
- Torsion TIP3P and TIP4P contains plumed.dat file which uses torsion angles as CVs (as described in the paper) to perform metadynamics simulations.
- PCA-TIP3P contains plumed.dat file which uses PC1 and PC2 as CVs to perform metadynamics simulations (see the paper for analyses and plots)
- COM TIP3P and TIP4P contains plumed.dat files to perform metadynamics simulations with centre of mass CVs (see full description in our paper).
Snapshots from clustering (using K-centers algorithm installed within Enspara) can be accessed here: https://www.dropbox.com/sh/xikqkkeiqajk9eu/AAAae-IkivyVXaqIbaloaLwqa?dl=0 The clustering was performed (using the build_msm.py script which can be accessed inside Clustering-script) on apo Plm-II using one of the MD trajectory with TIP3P water model.