Ryuichiro Ishitani

RGI-Toolkit: Differentiable Restraints for Controllable Biomolecular Structure Prediction

RGI-Toolkit enables controllable biomolecular structure prediction by integrating experimental restraints into diffusion models without retraining.

Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways

This paper introduces a distance-restraint-guided diffusion model to sample protein conformational changes and ligand dissociation pathways, achieving uniform coverage and high structural quality.

High-throughput prediction of protein-protein interactions uncovers hidden molecular networks in biosynthetic gene clusters

The paper predicts protein-protein interactions in biosynthetic gene clusters to uncover hidden molecular networks and functional enzyme complexes.

Multi-objective optimization for designing structurally similar proteins with diverse sequences

Structural basis of lipid-mediated gating in a two-pore domain potassium channel

This study presents the cryo-EM structure of TOK1, revealing its unique domain architecture and lipid-mediated gating mechanism through structural and functional analyses.

Improving Stereochemical Limitations in Protein-Ligand Complex Structure Prediction

This study improves stereochemical accuracy in protein-ligand complex structure prediction by addressing limitations in AlphaFold3 and Boltz-1 through a restraint-guided inference method.

Cryo-EM structure of the volume-regulated anion channel LRRC8

The paper presents the cryo-EM structure of the human LRRC8A protein, revealing its trimer-of-dimers assembly and structural features relevant to its function as a volume-regulated anion channel.