Dataset for "seekrflow: Towards an end-to-end automated simulation pipeline with machine-learned force fields for accelerated drug-target kinetic and thermodynamic predictions"

Dataset for "seekrflow: Towards an end-to-end automated simulation pipeline with machine-learned force fields for accelerated drug-target kinetic and thermodynamic predictions" This dataset was generated to validate the seekrflow automated end-to-end multiscale milestoning pipeline with machine-learned force fields for receptor-ligand complexes. It contains the simulation data used to compute kinetic rates and thermodynamic profiles for the following receptor-ligand complexes: Eight Heat Shock Protein 90 (HSP90) inhibitor complexes Eight Threonine-Tyrosine Kinase (TTK / Mps1) inhibitor complexes Trypsin-benzamidine complex (benchmark) The dataset is organized into three per-system directories. Each contains per-complex tarballs (one per receptor-ligand complex) and an analysis/ folder that bundles the scripts and outputs used to generate the manuscript figures and tables. seekrflow_HSP/│── 1.tar.gz # HSP90 inhibitor 1│── 6.tar.gz # HSP90 inhibitor 2│── 31.tar.gz # HSP90 inhibitor 3│── 37.tar.gz # HSP90 inhibitor 4│── 43.tar.gz # HSP90 inhibitor 5│── 62.tar.gz # HSP90 inhibitor 6│── 65.tar.gz # HSP90 inhibitor 7│── 70.tar.gz # HSP90 inhibitor 8│── analysis/ # SEEKR2 analysis pipeline for HSP90 seekrflow_TTK/│── 2X9E.tar.gz # TTK inhibitor 1│── 3GFW.tar.gz # TTK inhibitor 2│── 3H9F.tar.gz # TTK inhibitor 3│── 5LJJ.tar.gz # TTK inhibitor 4│── 5N7V.tar.gz # TTK inhibitor 5│── 5N84.tar.gz # TTK inhibitor 6│── 5N93.tar.gz # TTK inhibitor 7│── 5NAD.tar.gz # TTK inhibitor 8│── analysis/ # SEEKR2 analysis pipeline for TTK seekrflow_TRP/│── SEEKR_SIMULATION.tar.gz # trypsin-benzamidine simulation tree│── input.xml # seekrflow input configuration│── ligand.pqr # benzamidine structure (PQR)│── receptor.pqr # trypsin structure (PQR)│── receptor_ligand.xml # parameterized complex (OpenMM XML)│── analysis/ # SEEKR2 analysis pipeline for trypsin Each per-complex tarball expands to the following structure. <complex>/│── input.xml # seekrflow input configuration│── ligand.pqr # ligand structure (PQR)│── receptor.pqr # receptor structure (PQR)│── receptor_ligand.xml # parameterized complex (OpenMM XML)│── SEEKR_SIMULATION/│ │── model.xml # SEEKR2 milestoning parameters│ │── anchor_0/ ... anchor_15/ # one directory per Voronoi cell│ │ │── building/ # per-anchor topology and restart files│ │ │── prod/│ │ │ │── mmvt1.dcd # production MD trajectory│ │ │ │── mmvt.restart1.out # transition count file│ │ │ │── backup.checkpoint # simulation checkpoint│ │── images_and_plots/ # per-complex figures and rates.out The analysis/ folder for each system contains the driver script run_all.py plus stage-specific Python scripts (run_analyze.py, run_convergence.py, compare.py, get_free_energy.py, plot_free_energy.py, plot_convergence.py, and plot_taus.py), an analysis_files/ directory with text outputs from the SEEKR2 analyzer, and an analysis_figures/ directory with the figures reproduced from those outputs. To reproduce the manuscript results for one protein system (HSP90 shown as an example): cd seekrflow_HSPfor f in *.tar.gz; do tar -xzf "$f"; donecd analysispython run_all.py The same workflow applies to TTK and trypsin-benzamidine complexes using their respective per-system directories. SEEKR2 must be installed and importable from the Python environment used to run run_all.py (see https://github.com/seekrcentral/seekr2 for installation instructions).