Full Data Download

CpuPDB Downloads

CpuPDB data are organized into three pocket structure archives and one trajectory file. All packages are provided through downloadable archives for pocket structures, LVpocket predictions, and trajectory data.

Cavities Data 5.88 GB

Experimentally verified ligand binding cavities from high-quality protein-ligand complexes.

Cryptic Pockets 1.26 GB

Dynamic cryptic pocket folders derived from molecular dynamics simulations.

LVpocket Data 12.20 GB

Predicted ligandable volume pocket structures from the CpuPDB LVpocket workflow.

Trajectory Data 47.98 GB

MD trajectories are distributed as a single HDF5 file.

Dataset Packages

Download the complete structure archives, LVpocket archive, and trajectory file from the table below.

Package Included Data Records Size Access
Cavities.zip Experimentally verified ligand binding cavities
  • Protein structure files
  • Cavity files defined around ligand binding sites
  • High-quality protein-ligand complex cavities
 38,781 independent folders 5.88 GB5.47 GiB Download
Cryptic_pockets.zip Dynamic cryptic pocket archive
  • Cryptic binding site structural files
  • Folders derived from molecular dynamics simulations
 5,515 folders 1.26 GB1.18 GiB Download
LVpockets.zip LVpocket predicted pocket archive
  • LVpocket predicted pocket structure files
  • Ligandable volume pocket folders for CpuPDB entries
  • Archive generated by the CpuPDB LVpocket workflow
 LVpocket folders 12.20 GB11.36 GiB Download
MD.h5 Molecular dynamics trajectory file
20 ns molecular dynamics trajectories with 200 frames per protein-ligand complex. MD5: 031475c87869edd6237aca33011b9e32 Trajectory data 47.98 GB44.68 GiB Download