European journal of medicinal chemistry
Sep 8, 2025
Accurate prediction of drug-target binding affinity is crucial for efficient drug discovery and design, enabling researchers to better understand molecular interactions and accelerate the identification of promising drug candidates. Despite recent ad...
Molecular interaction networks are a vital tool for studying biological systems. While many tools exist that visualize a protein or a pathway within a network, no tool provides the ability for a researcher to consider a protein's position in a networ...
Journal of chemical information and modeling
Sep 4, 2025
Lipids are essential metabolites that play critical roles in multiple cellular pathways. Like many primary metabolites, mutations that disrupt lipid synthesis can be lethal. Proteins involved in lipid synthesis, trafficking, and modification, are tar...
Journal of chemical information and modeling
Sep 3, 2025
Proteochemometric models (PCMs) are used in computational drug discovery to employ both protein and ligand representations jointly for bioactivity prediction. While machine learning (ML) and deep learning (DL) have come to dominate PCMs, often servin...
The secondary structure of a protein serves as the foundation for constructing its three-dimensional (3D) structure, which in turn is critical for determining its function and role in biological processes. Therefore, accurately predicting secondary s...
Journal of chemical theory and computation
Aug 29, 2025
Development of suitable scoring functions is essential for the prediction of RNA-protein complex structures. Conventional statistical potential-based scoring functions suffered from deficiencies in handling conformational flexibility. The recent appl...
Phenotypic screening is undergoing a resurgence in the field of targeted protein degradation as a powerful complement to target-based approaches, which are often constrained by requirements for detailed structural and ligand-binding information. Phen...
Journal of chemical information and modeling
Aug 25, 2025
Accurate prediction of the peptide-protein interaction (PepPI) is crucial for developing peptide-based therapeutics and vaccines. However, this computational task has traditionally faced significant challenges, such as the scarcity of structure data ...
Journal of chemical information and modeling
Aug 21, 2025
Predicting compound-protein interaction (CPI) plays a critical role in drug discovery and development, but traditional screening experiments consume much time and resources. Therefore, deep learning methods for CPI prediction are popular now. However...
Proceedings of the National Academy of Sciences of the United States of America
Aug 20, 2025
The rapid expansion of protein sequence and structure databases has resulted in a significant number of proteins with ambiguous or unknown function. While advances in machine learning techniques hold great potential to fill this annotation gap, curre...
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