Enhanced Sampling of Protein Conformational Changes via True Reaction Coordinates from Energy Relaxation

The dataset contains RC-uncovered and natural reactive trajectories. Coordinates of water molecules are excluded to reduce data size. It also contains initial and final structures for all trajectories in PDB format.

Data Description

The data are provided as one .zip file. It can be unzipped by running unzip traj_data.zip

Trajectories are provided as .xtc files. Initial structures are provided as *-Initial.pdb, and final structures are provided as *-Final.pdb.

Two types of trajectories are provided, with RC-covered trajectories labeled as *RC-uncov* and natural reactive trajectories labeled as *NRT*.

The dataset includes trajectories for three systems, each labeled as follows:

DRV-bound HIV-PR is labeled as DRV*

MA/CA-bound HIV-PR is labeled as MA-CA*

PDZ domain is labeled as PDZ*

Moreover, force field files of the three systems are provided in the directories DRV_ff, MA-CA_ff, and PDZ_ff.

Custom Code

Custom code for generalized work functional approach and custom GROMACS code for generating RC-uncovered trajectories are provided on Code Ocean (https://codeocean.com/capsule/6873439/tree).