Abstract: A system and method for generating customizable molecular structures for drug discovery. The system includes a processor communicably coupled to a memory and executes a deep neural network based molecular encoding model. The processor receives input datasets of drug-like molecules from private and public databases and are employed as training dataset. The processor further executes a plurality of deep generative models configured to receive input data relating to small molecules which includes desirable molecules and undesirable molecules. The plurality of deep generative models generates molecular structures like the input desirable molecules. The deep neural network based molecular encoding model is configured to map similarities between the molecular structures generated. The deep neural network based molecular encoding model computes intra-model and inter-model distances.

Abstract: A system for generating a novel molecular structure using a protein structure is disclosed. One or more processors generate a protein voxel representation of a protein structure that includes a multichannel three-dimensional (3D) grid that includes a plurality of channels. A cavity region is detected in the protein voxel representation based on a combination of rule-based detection and a deep learning based model. A cavity voxel representation of the cavity region is generated based on upscaling of a regional voxel of the detected cavity region. A ligand voxel representation of a ligand structure is generated based on the cavity voxel representation. A 3D voxel descriptor is determined for a protein-ligand complex based on the protein voxel representation and the ligand voxel representation. A simplified molecular-input line-entry system (SMILES) of a novel molecular structure is generated using a rich 3D embedding vector, which is based on the 3D voxel descriptor.