Summary Understanding the binding site of the target protein is essential for rational drug design. Pocket detection software predicts the ligand binding site of the target protein; however, the predicted protein pockets are often excessively estimated in comparison with the actual volume of the bound ligands. This study proposes a refinement tool for the pockets predicted by an alpha sphere-based approach, Pocket to Concavity (P2C). P2C is divided into two modes: Ligand-Free (LF) and Ligand-Bound (LB) modes. The LF mode provides the shape of the deep and druggable concavity where the core scaffold can bind. The LB mode searches the deep concavity around the bound ligand. Thus, P2C is useful for identifying and designing desirable compounds in Structure-Based Drug Design (SBDD). Availability and implementation Pocket to Concavity is freely available at https://github.com/genki-kudo/Pocket-to-Concavity. This tool is implemented in Python3 and Fpocket2. Supplementary information Supplementary data are available at Bioinformatics online.

Problem statement: Though alloxan-induced mouse hyperglycemia was ameliorated by feeding of 5 % Asperagillus awamori (A. awamori)-fermented burdock root diet (fermented burdock diet), it is unclear whether the anti-hyperglycemia activity is due to A. awamori or antioxidant activity induced by the fermentation.Methods: A 0.05 % A. awamori diet was prepared. Acatalasemic mice, having a quite low catalase activity in blood, were divided three groups, and each group fed control, A. awamori and the fermented burdock diets for 14 weeks, separately. Then, alloxan monohydrate (200 mg/ kg of body weight) was intraperitoneally administrated to each mouse. Glucose, insulin, C-peptide contents in blood and glucose tolerance tests (GTTs) were examined.Results: Incidence of alloxan-induced hyperglycemia in acatalasemic mice maintained with the A. awamori diet or the fermented burdock diet was low (20 or 25%) compared to that (75%) maintained with the control diet. Feeding the A. awamori diet ameliorated insulin, C-peptide in blood and GTT like as mice fed the fermented burdock diet. It indicated that A. awamori in these diets plays an important role for the prevention of alloxan-induced hyperglycemia.Conclusions: It is suggested that A. awamori has the anti-hyperglycemia activity.

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