International journal of biological macromolecules
May 30, 2025
The present work shows a computational approach to assess the interactions of different nature-inspired peptides with hair keratin models. An updated keratin model was validated, and comparisons with previous models were traced, thereby highlighting ...
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
Journal of chemical information and modeling
May 22, 2025
Docking-based virtual screening tools customized to mine ultralarge chemical spaces are consistently reported to yield both higher hit rates and more potent ligands than that achieved by conventional docking of smaller million-sized compound librarie...
Understanding the interaction between T Cell Receptors (TCRs) and peptide-bound Major Histocompatibility Complexes (pMHCs) is crucial for comprehending immune responses and developing targeted immunotherapies. While recent machine learning (ML) model...
The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs us...
BACKGROUND: Predicting protein-DNA binding sites in vivo is a challenging but urgent task in many fields such as drug design and development. Most promoters contain many transcription factor (TF) binding sites, yet only a few have been identified thr...
Understanding how genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F crosses with extensive genetic diversity...
Journal of chemical information and modeling
May 1, 2025
Heat shock protein 90 (Hsp90) is a pivotal molecular chaperone crucial in the maturation of client proteins, positioning it as a significant target for cancer therapy. However, the design of effective Hsp90 inhibitors presents substantial challenges ...
International journal of biological macromolecules
Apr 30, 2025
Predicting protein-ligand binding affinity is crucial for drug discovery. However, existing prediction methods often make insufficient use of the features of proteins and ligands, lack interactions between different information, and have difficulty i...
Transthyretin (TTR) plays a vital role in thyroid hormone transport and homeostasis in both the blood and target tissues. Interactions between exogenous compounds and TTR can disrupt the function of the endocrine system, potentially causing toxicity....
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