Antioxidant peptides derived from dietary proteins positively impact human health due to their high activity and safety. In this study, a database of 76,343 peptides was constructed via in silico hydrolysis of 29 dietary proteins. A novel antioxidant...
Journal of chemical information and modeling
Aug 6, 2025
The coronavirus main protease, essential for viral replication, is a well-validated antiviral target. Here, we present Deep-CovBoost, a computational pipeline integrating deep learning with free energy perturbation (FEP) simulations to guide the stru...
Journal of chemical theory and computation
Aug 5, 2025
Binding free energies are key elements in understanding and predicting the strength of protein-drug interactions. While classical free energy simulations yield good results for many purely organic ligands, drugs, including transition metal atoms, oft...
Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie
Aug 2, 2025
Despite therapeutic advancements, metastatic and nonmetastatic castration-resistant prostate cancer (mCRPC and nmCRPC) remain incurable due to drug resistance, partly due to Androgen receptor (AR) gene abnormalities and splice variants. An Augmented ...
Protein aggregation is one of the key challenges in the biopharmaceutical industry as its control is crucial in achieving long-term stability and efficacy of biopharmaceuticals. Attempts have been made to develop regression models for predicting the ...
Pholiota adiposa is recognized for its health benefits, particularly in Alzheimer's disease (AD), but its molecular mechanism remains elusive. Our study employs network pharmacology and machine learning to uncover its therapeutic potential. We constr...
The global rise of antibiotic-resistant infections has been driven in part by the spread of bacteria producing metallo-β-lactamase (MBL), particularly New Delhi metallo-β-lactamase-1 (NDM-1). Currently, there are no clinically approved inhibitors tar...
Solubility is critical in drug discovery and development, as it significantly influences a medication's bioavailability and therapeutic efficacy. Understanding solubility at the early stages of drug discovery is essential for minimizing resource cons...
Journal of physics. Condensed matter : an Institute of Physics journal
Jul 23, 2025
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and analysis f...
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics, but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar pr...
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