Masakazu Sekijima

VisINet — trained SARS-CoV-2 Mpro model

Nobuaki Yasuo, HIROSHI YODA, Kazuki Yamamoto, Masakazu Sekijima

This is the trained VisINet model used for the prospective SARS-CoV-2 main protease (Mpro)virtual screening reported in: > Yasuo, N.; Yoda, H.; Yamamoto, K. Z.; Sekijima, M. *VisINet: Prospective> Structure-Based Virtual Screening Identifies SARS-CoV-2 Main Protease Hit Compounds.* VisINet is an image-based …

jp (code pays fourni par la source)

VisINet — trained SARS-CoV-2 Mpro model

Nobuaki Yasuo, HIROSHI YODA, Kazuki Yamamoto, Masakazu Sekijima

This is the trained VisINet model used for the prospective SARS-CoV-2 main protease (Mpro)virtual screening reported in: > Yasuo, N.; Yoda, H.; Yamamoto, K. Z.; Sekijima, M. *VisINet: Prospective> Structure-Based Virtual Screening Identifies SARS-CoV-2 Main Protease Hit Compounds.* VisINet is an image-based …

jp (code pays fourni par la source)

A Transformer for Reaction-Aware Compound Explorations with GFlowNet in QSAR-Guided Molecular Design

Shōgo Nakamura, Nobuaki Yasuo, Masakazu Sekijima

In drug discovery tasks, achieving a balance between high biological activity toward therapeutic targets and synthetic chemical feasibility is critically important. While the recently proposed deep learning-based molecular generation models have enabled explorations of vast chemical spaces, most existing approaches do not …

jp, us (code pays fourni par la source)

Interaction-constrained 3D molecular generation using a diffusion model enables structure-based pharmacophore modeling for drug design

Masami Sako, Nobuaki Yasuo, Masakazu Sekijima

Abstract A key challenge in structure-based drug design is generating three-dimensional molecules while preserving essential protein-ligand interactions. We propose DiffPharma, a structure-based pharmacophore modeling framework based on a conditional diffusion model, to generate molecules that satisfy specified interaction constraints. The proposed method …

jp (code pays fourni par la source)

Incorporating Angular Information Into GNNs for Protein-Protein Interaction Re-ranking

Yukinobu Matsuno, Nobuaki Yasuo, Masakazu Sekijima

jp (code pays fourni par la source)

Interaction-constrained 3D molecular generationusing a diffusion model enables structure-basedpharmacophore modeling for drug design

Masami Sako, Nobuaki Yasuo, Masakazu Sekijima

A key challenge in structure-based drug design is generating three-dimensional molecules while preserving essential protein-ligand interactions. We propose DiffPharma, a structure-based pharmacophore modeling framework based on a conditional diffusion model, to generate molecules that satisfy specified interaction constraints. The proposed method incorporates …

jp (code pays fourni par la source)

Protective function of the voltage-gated potassium channel Kv11.3 in a mouse model of cardiac ischemia/reperfusion injury

Hayato Sasaki, Kazuki Otake, Kazuki Takeda, Karin Tesaki et autres

Voltage-gated potassium (Kv) channels contribute to repolarization in excitable tissues such as nerves and cardiac muscle; consequently, they control the firing frequency and duration of action potential. Their dysfunction can thus cause neurological disorders and cardiac disorders with arrhythmias. The dysfunction of …

jp (code pays fourni par la source)

Molecular optimization using a conditional transformer for reaction-aware compound exploration with reinforcement learning

Shōgo Nakamura, Nobuaki Yasuo, Masakazu Sekijima

Designing molecules with desirable properties is a critical endeavor in drug discovery. Because of recent advances in deep learning, molecular generative models have been developed. However, the existing compound exploration models often disregard the important issue of ensuring the feasibility of organic …

jp (code pays fourni par la source)

Development of tolerance to bedaquiline by overexpression of trypanosomal acetate: succinate CoA transferase in Mycobacterium smegmatis

Gloria Mavinga Bundutidi, Kota Mochizuki, Yuichi Matsuo, Mizuki Hayashishita et autres

The F-type ATP synthase inhibitor bedaquiline (BDQ) is a potent inhibitor of mycobacterial growth and this inhibition cannot be rescued by fermentable carbon sources that would supply ATP by an alternative pathway (substrate level phosphorylation). To gain mechanistic insight into this phenomenon, …

République démocratique du Congo, jp, nz, fr, de (code pays fourni par la source)

Comprehensive Molecular Docking on the AlphaFold-Predicted Protein Structure Proteome: Identifying Target Protein Candidates for Puberulic Acid, a Suspected Lethal Nephrotoxin

Ryo Kamata, Masakazu Sekijima, Kazuki Takeda

Abstract This study presents a novel in silico screening method for identifying potential protein-ligand interactions within the complete structural proteome, as predicted by AlphaFold2, using puberulic acid as a test case. The methodology utilizes molecular docking simulations to predict interactions based on …

jp (code pays fourni par la source)

PRA-MutPred: Predicting the Effect of Point Mutations in Protein–RNA Complexes Using Structural Features

K. Harini, Masakazu Sekijima, M. Michael Gromiha

Interactions between proteins and RNAs are essential for the proper functioning of cells, and mutations in these molecules may lead to diseases. These protein mutations alter the strength of interactions between the protein and RNA, generally described as binding affinity (Δ G …

in, jp, Afrique du Sud (code pays fourni par la source)

Comprehensive molecular docking on the AlphaFold-predicted protein structure proteome: identifying target protein candidates for puberulic acid

Ryo Kamata, Masakazu Sekijima, Kazuki Takeda

Identifying the molecular targets of toxic compounds remains a major challenge in toxicology, particularly when adverse effects occur in off-target organs and the mechanism of action is unknown. To address this issue, a comprehensive computational pipeline was developed to perform high-throughput molecular …

jp (code pays fourni par la source)