EMSPLA for accurate feature molecular extraction from protein-ligand interactions

Abstract

Protein-ligand interactions are fundamental in various biological and medical fields, influencing drug discovery and therapeutic development. In recent years, deep learning (DL) has revolutionized the study of these interactions, but significant challenges remain in accurately representing molecular structures for DL models. Traditional featurization techniques often depend on handcrafted features, requiring expert knowledge and potentially missing crucial molecular aspects. This work addresses these challenges by developing and evaluating a novel protein-ligand feature extraction system using an enhanced molecular similarity protein-ligand aligner (EMSPLA). The primary objective is to leverage EMSPLA for similarity matching in protein-ligand interactions, improving predictive model accuracy. The methodology combines convolutional neural networks (CNN) for local feature extraction with an attention module to capture long-distance dependencies, enhancing binding site predictions. Using the PDBbind v.2020 dataset, the EMSPLA model demonstrated superior performance with a root mean square error (RMSE) of 0.67, surpassing current state-of-the-art models. These findings highlight the system’s potential for efficient deployment and scalability, positioning it as a powerful tool in computational biology and drug discovery, ultimately advancing our understanding of protein-ligand interactions.