Dataset for automated milestoning simulations for receptor-ligand complexes with machine-learned force fields

Dataset for automated milestoning simulations for receptor-ligand complexes with machine-learned force fields

This dataset was generated to validate the automated milestoning computational pipeline with machine-learned force fields for receptor-ligand complexes. This dataset contains simulation data generated employing the automated multiscale milestoning framework with machine-learned force fields to compute the kinetics and thermodynamics of ligand unbinding for multiple receptor-ligand complexes. The dataset includes per-milestone trajectories, parameter file (model.xml), kinetic rates, and thermodynamic analysis results (images_and_plots) for the following complexes:

Eight Threonine-Tyrosine Kinase (TTK) complexes

Eight Heat Shock Protein 90 (HSP90) complexes

Trypsin-benzamidine Complex

Each complex directory (TTK_complexes, HSP90_complexes, Trypsin_benzamidine) contains directories labeled 1 through 8 (for TTK and HSP90), corresponding to different inhibitor-ligand pairs studied in the manuscript.

data_automated_milestoning

│── TTK_complexes/

│ ├── 1/

│ ├── 2/

│ ├── 3/

│ ├── 4/

│ ├── 5/

│ ├── 6/

│ ├── 7/

│ ├── 8/

│── HSP90_complexes/

│ ├── 1/

│ ├── 2/

│ ├── 3/

│ ├── 4/

│ ├── 5/

│ ├── 6/

│ ├── 7/

│ ├── 8/

│── Trypsin_benzamidine/

Each directory within TTK_complexes (1-8), HSP90_complexes (1-8), and Trypsin_benzamidine contains the following structure:

│── 1/ (receptor_inhibitor complex)

│ ├── anchor_0/

│ │ ├── building/

│ │ │ ├── Topology PDB file

│ │ │ ├── Restart OpenMM XML file

│ │ ├── prod/

│ │ │ ├── Trajectory DCD file

│ │ │ ├── mmvt1.dcd # Simulation trajectory DCD file

│ │ │ ├── backup.checkpoint # Simulation checkpoint file

│ │ │ ├── mmvt.restart1.out # Transition count file

│ ├── anchor_1/

│ ├── anchor_2/

│ ├── ...

│ ├── ...

│ ├── anchor_15/

│ ├── model.xml # Milestoning simulation XML parameter file

│ ├── images_and_plots/

│ │ ├── free_energy_profile_anchor.png # Free energy plot

│ │ ├── free_energy_profile_milestones.png # Milestone-wise free energy

│ │ ├── milestone_free_energy.txt # Free energy values at each milestone

│ │ ├── rates.out # Computed kinetic rates (koff)

│ │ ├── transition_matrices/ # Transition statistics files

│ │ │ ├── N_ij_alpha

│ │ │ ├── N_alpha_beta

│ │ │ ├── T_alpha

│ │ │ ├── R_i_alpha

│ │ │ ├── pi_alpha.png

│ │ ├── pi_alpha. # Stationary probabilities of milestones

│ │ ├── p_i.png # Probability distribution

│ │ ├── k_alpha_beta # Kinetic transition rates

All data has been compressed into a single zip file named data_automated_milestoning.zip for easier storage and transfer.