PocketLG: Protein Binding Pocket Identification Using Protein Language Model and Graph Transformer

Protein pocket is a special region on the surface of a protein that commonly interacts with other molecules, especially small molecule compounds. Accurately identifying and understanding the structure character of protein pockets, that can accelerate the development of new drugs, as well improve existing drugs to reveal disease mechanisms. In this study, we propose a deep learning method named PocketLG, to identify the potential binding pockets integrating a Protein Language model and Graph Transformer. The method constructs the pocket identification task as a regression problem, which can more accurately identify the real pocket boundaries. In addition, We propose a data sampling strategy and construct a pipeline to support the data sampling effort. This strategy has the benefit of augmenting the data, allowing the model to better learn the intrinsic characteristics of the pocket structure, even for pockets with unknown boundaries This method can sample the unknown pocket by dividing different sample sizes and then determine the boundary of the unknown pocket by the regression value, it can be a direct help for downstream tasks. Experimental results show that our deep learning model can identify binding pockets on proteins with 91 percent success rate. This work provides a new technical route for protein binding pocket prediction research, which can greatly contribute to the development of the pharmaceutical industry. PocketLG source code, pre-trained models and data preprocessing code are available at https://github.com/NENUBioCompute/PocketLG.