Journal of chemical information and modeling
Sep 19, 2025
Protein-protein interactions (PPIs) play fundamental roles in biological processes and therapeutic development. Accurately predicting PPI binding affinity is critical for understanding interaction mechanisms and guiding protein engineering. Recent ad...
Journal of chemical information and modeling
Sep 19, 2025
Drug-target interaction (DTI) prediction plays a pivotal role in drug discovery. In recent years, deep learning-based models have been advanced rapidly, accelerating the identification of potential DTIs. However, how to effectively capture the cross-...
Journal of chemical information and modeling
Sep 18, 2025
Protein-protein interactions play pivotal roles in a wide range of biological processes. Determining the atomic-level structures of protein-protein complexes is indispensable for elucidating macromolecular interaction mechanisms and advancing structu...
Journal of chemical information and modeling
Sep 17, 2025
Molecular dynamics simulations based on coarse-grained (CG) models are used to accelerate conformational dynamics of biomolecules and other chemical systems with reduced computational costs. CG models achieve this by discarding atomic information nec...
Journal of chemical information and modeling
Sep 17, 2025
Free energy perturbation (FEP) methods are among the most accurate tools in structure-based drug design for predicting protein-ligand binding affinities. However, their adoption remains limited due to high computational demands and complex setup proc...
Journal of chemical information and modeling
Sep 16, 2025
Protein-ligand binding affinity assessment plays a pivotal role in virtual drug screening, yet conventional data-driven approaches rely heavily on limited protein-ligand crystal structures. Structure-free compound-protein interaction (CPI) methods ha...
Journal of chemical information and modeling
Sep 16, 2025
Rigid docking remains the most popular method of predicting protein-protein interactions in cases when experimental 3D structures of the complexes are not available. The docking often relies on known unbound (Apo) protein structures, which may differ...
Journal of chemical information and modeling
Sep 16, 2025
Sequence-based drug-target interaction (DTI) prediction is an effective approach for identifying potential drug candidates without relying on three-dimensional protein structures. However, current sequence-based methods often suffer from limited gene...
Journal of chemical information and modeling
Sep 11, 2025
Protein-nucleic acid interactions are fundamental to biological processes and biotechnology, yet their computational prediction lags behind protein structure or protein-protein interaction modeling. This study introduces ProNASet, a benchmark data se...
Computational methods have revolutionized NMR spectroscopy, driving significant advancements in structural biology and related fields. This review focuses on recent developments in quantum chemical and machine learning approaches for computational NM...
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