APObind: A Dataset of Ligand Unbound Protein Conformations for Machine Learning Applications in De Novo Drug Design

A drawback of these methods that perform important tasks related to methods however is that, they tend not to generalise well drug design such as receptor binding site detection, to data that does not resemble the data distribution used for small molecule docking and binding affinity training. The viability of such models therefore depend on prediction. However, these methods are usually well curated training data that translates well into real world trained on only ligand bound (or holo) conformations applications. of the protein and therefore are not guaranteed to perform well when the protein structure Deep Learning models pertaining to SBDD workflows are is in its native unbound conformation (or apo), usually trained on datasets containing 3D structures of which is usually the conformation available for protein-ligand complexes (Batool et al., 2019). PDBbind a newly identified receptor. A primary reason (Wang et al., 2005) is a predominantly used dataset that provides for this is that the local structure of the binding experimental binding affinity values for protein-ligand site usually changes upon ligand binding. To facilitate co-crystal structures present in the Protein Data Bank (PDB) solutions for this problem, we propose a (Berman et al., 2000). Deep learning architectures usually dataset called APObind that aims to provide apo use voxelized (Jiménez et al., 2018) or graph like representations conformations of proteins present in the PDBbind (Son & Kim, 2021) of the 3D structures present in dataset, a popular dataset used in drug design. Furthermore, PDBbind for computation to get benchmark performances.