AI3 Protein-Ligand Binding Affinity Dataset

The rapid advancement of computing technologies, particularly artificial intelligence (AI), has revolutionized various domains, including drug discovery. Curated datasets are crucial for developing reliable, generalizable, and accurate models for practical applications. Generating experimental data on a large scale is an expensive and arduous process. In domains such as medical diagnostics where real-life data is hard to obtain, synthetic data has been shown to be extremely valuable. We, teams from IIIT Hyderabad, Intel, AWS, and Insilico Medicine, have performed physics-based calculations (molecular dynamics simulations) on about 20,000 protein-ligand complexes. The dataset comprises molecular dynamics snapshots, binding affinities calculated using the MM-PBSA method, and individual energy components, including electrostatic and van der Waals interactions. DatasetFileFormats essentially incorporate i. 3D coordinates of the protein-ligand complexes (pdb) in tar.gz files, and ii. CSV files containing the energy data. DatasetUsages are on i. ML scoring function for predicting binding affinities of given protein-ligand complexes, ii. Classification models for predicting correct binding poses of ligands, iii. identification of cryptic binding pockets, and iv. optimization of binding features by exploiting the individual components of the energy (experimental data has only the total binding affinity). Further, the novelty of the dataset highlights the fact that existing AI/ML training datasets lack dynamic data and are inherently biased. Further, binding affinity data existing in the literature are obtained from different experimental protocols. Therefore, this dataset has been uniquely created (from the same computational protocols) followed by free energy calculations with molecular dynamics (MD) simulations. The dynamic data-enriched protein-ligand coordinates can be used to effectively train convolutional neural network-based regression models for more accurate binding affinity prediction.