CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function

Abstract

Protein-carbohydrate interactions are crucial for many cellular processes but can be challenging to biologically characterise. To improve our understanding and ability to model these molecular interactions, we used a carefully curated set of 370 protein-carbohydrate complexes with experimental structural and biophysical data in order to train and validate a new tool, cutoff scanning matrix (CSM)-carbohydrate, using machine learning algorithms to accurately predict their binding affinity and rank docking poses as a scoring function. Information on both protein and carbohydrate complementarity, in terms of shape and chemistry, was captured using graph-based structural signatures. Across both t..