Hydration is necessary for protein folding, stability, and functions. The hydration structure of proteins is formed inside proteins and at the interfaces between bulk solvent and protein, and has been visualized mostly using cryogenic X-ray crystallography. From massive structural data of proteins with hydration structures, we developed a three-dimensional convolutional network to generate distributions of the existence probability of hydration water molecules on protein surfaces and in protein cavities. We also devised a positional search method of hydration water molecules based on the probability maps. The predicted hydration sites are located on an average within 0.3 Å from the experimentally identified sites in crystal structures.

Protein design has become a central focus in contemporary biology and chemistry. This review highlights recent advances in protein redesign, a strategy that generates artificial proteins by introducing multiple mutations into template protein. We first examine sequence‑based approaches—ancestral sequence reconstruction （ASR） and consensus design （CD）—that are now widely adopted. We then discuss two next‑generation methods: （i） hybrid strategies that couple CD with structure‑guided rational design, and （ii） state‑of‑the‑art platforms that integrate generative artificial intelligence with conventional redesign workflows.

The biological functions of macromolecules are closely associated with their three-dimensional structures and corresponding electronic states. Quantum chemical calculations are an approach that can determine electronic states from first principles without relying on empirical parameters. In this study, we present a quantum mechanics-based dataset derived from representative structures curated in SCOP2. The calculations were performed using the fragment molecular orbital（FMO）method, which is applicable to large biomolecules such as proteins. The dataset comprises total energies for approximately 5,000 structures and over 200 million inter-fragment interaction energies, including electrostatic and dispersion components. This resource is expected to support functional analyses based on electronic structure and to facilitate machine learning studies in biomolecular interaction studies.

Fertilization is the process by which male and female gametes fuse to form a fertilized egg. In mammals and amphibians, polyspermy is lethal. Upon fertilization, egg-derived proteases specifically cleave ZP2, one of the glycoproteins surrounding the oocyte, associated with egg coat hardening. However, the molecular mechanisms and egg coat structure remained unknown. We combined X-ray crystallography, cryo-electron microscopy, and AlphaFold2 structure prediction to elucidate the three-dimensional structure of egg coat matrix formed by ZP glycoprotein polymerization and the molecular mechanisms underlying polyspermy block through egg coat structural changes.

ReciPro is a free and open-source graphical-user-interface-based crystallographic software that provides seamless access to functions to explore crystal databases, visualize crystal structures and goniometer settings, simulate diffraction patterns and high-resolution microscope images, and analyze diffraction data. These features are linked through a user-friendly GUI, and the results can be synchronously displayed almost in real time. ReciPro will assist a wide range of crystallographers（including beginners）using X-ray, electron and neutron diffraction crystallography and TEM.