SHREC 2022: Protein-ligand binding site recognition (2206.06035v4)

Abstract: This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition. The prediction of protein-ligand binding regions is an active research domain in computational biophysics and structural biology and plays a relevant role for molecular docking and drug design. The goal of the contest is to assess the effectiveness of computational methods in recognizing ligand binding sites in a protein based on its geometrical structure. Performances of the segmentation algorithms are analyzed according to two evaluation scores describing the capacity of a putative pocket to contact a ligand and to pinpoint the correct binding region. Despite some methods perform remarkably, we show that simple non-machine-learning approaches remain very competitive against data-driven algorithms. In general, the task of pocket detection remains a challenging learning problem which suffers of intrinsic difficulties due to the lack of negative examples (data imbalance problem).