HTML Website Builder5,000 protein-ligand complexes selected from the Protein Data Bank (PDB). For each complex, it offers binding affinity data along with energy components—such as electrostatic, van der Waals, polar, and non-polar solvation energies—calculated via Molecular Dynamics (MD) simulations using the MMPBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. There are two variations of the dataset:
This work has been published in Scientific Data: https://doi.org/10.1038/s41597-022-01631-9
Link to datasets
An additional 15,000 protein-ligand complexes were added to the PLAS 5K dataset to create the PLAS 20 K
This work was also published in Scientific Data: https://doi.org/10.1038/s41597-023-02872-y
Link to datasets
Collaborative effort from IIIT Hyderabad, Intel, AWS, and Insilico Medicine, we have conducted physics-based calculations (molecular dynamics simulations) on approximately 20,000 protein-ligand complexes. The resulting dataset includes molecular dynamics snapshots, binding affinities calculated using the MM-PBSA method, and individual energy components such as electrostatic and van der Waals interactions.
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A dataset of ligand-unbound protein conformations for machine learning applications in de novo drug design was created. Ligand-free protein structure equivalents for 10,599 out of 16,608 protein-ligand complexes were sourced from the PDBbind v.2019 database. This effort aimed to facilitate computation and large-scale validation of structure-based drug design methods using apo structures. The ligand-free structures were identified by mining the PDB database for apo protein structures that showed strong sequence and structural alignment with the proteins found in PDBbind.
Link to dataset
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