Predicting therapeutic and side effects from drug binding affinities to human proteome structures

Sawada, Ryusuke; Sakajiri, Yuko; Shibata, Tomokazu; Yamanishi, Yoshihiro

doi:10.1016/j.isci.2024.110032

iScience

2024

DOI: 10.1016/j.isci.2024.110032

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Predicting therapeutic and side effects from drug binding affinities to human proteome structures

Ryusuke Sawada,

Yuko Sakajiri,

Tomokazu Shibata

et al.

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Cited by 2 publications

References 113 publications

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Interactive multi-hypergraph inferring and channel-enhanced and attribute-enhanced learning for drug-related side effect prediction

Xuan,

Wu,

Cui

et al. 2025

Computers in Biology and Medicine

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Interactive multi-hypergraph inferring and channel-enhanced and attribute-enhanced learning for drug-related side effect prediction

Xuan,

Wu,

Cui

et al. 2025

Computers in Biology and Medicine

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ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

Nguyen,

2024

Structural Dynamics

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Proteins, serving as the fundamental architects of biological processes, interact with ligands to perform a myriad of functions essential for life. Designing functional ligand-binding proteins is pivotal for advancing drug development and enhancing therapeutic efficacy. In this study, we introduce ProteinReDiff, an diffusion framework targeting the redesign of ligand-binding proteins. Using equivariant diffusion-based generative models, ProteinReDiff enables the creation of high-affinity ligand-binding proteins without the need for detailed structural information, leveraging instead the potential of initial protein sequences and ligand SMILES strings. Our evaluations across sequence diversity, structural preservation, and ligand binding affinity underscore ProteinReDiff's potential to advance computational drug discovery and protein engineering.

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Predicting therapeutic and side effects from drug binding affinities to human proteome structures

Cited by 2 publications

References 113 publications

Interactive multi-hypergraph inferring and channel-enhanced and attribute-enhanced learning for drug-related side effect prediction

Interactive multi-hypergraph inferring and channel-enhanced and attribute-enhanced learning for drug-related side effect prediction

ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

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