In this work we introduce TorchANI-Amber, an interface for routine molecular dynamics simulations of biomolecular systems using ANI-style machine learning potentials. TochANI-Amber incorporates the ANI neural network potentials into the Amber softwar...
The rapid development of machine learning (ML) and deep learning (DL) methods provides new opportunities for innovative drug discovery. While these techniques are widely used in docking organic molecules (drugs) with protein, an evaluation of the per...
The CRISPR/Cas9 system is a powerful gene-editing tool. Its specificity and stability rely on complex allosteric regulation. Understanding these allosteric regulations is essential for developing high-fidelity Cas9 variants with reduced off-target ef...
Journal of computer-aided molecular design
Nov 8, 2025
The overexpression or activation of C-terminal Src kinase (CSK) has been recognized as a pivotal factor in the progression of hepatocellular carcinoma (HCC), positioning CSK as a promising therapeutic target. Despite this potential, no CSK-specific i...
Journal of chemical information and modeling
Nov 6, 2025
The sigma-2 receptor (σR/TMEM97) is a clinically relevant membrane protein involved in cholesterol regulation and overexpressed in cancer and neurodegenerative diseases. Despite its therapeutic potential, the dynamic mechanisms underlying σR function...
Physical chemistry chemical physics : PCCP
Nov 5, 2025
Protein stability plays a critical role in structural elucidation, enzyme activity, and the storage of protein drugs, where ionic liquids (ILs) have emerged as promising protein stabilizers due to their exceptional biocompatibility and superior solub...
Journal of chemical information and modeling
Nov 4, 2025
Protein and protein-protein complex conformations play a critical role in biological functions, while exploring these via traditional molecular dynamics (MD) simulation is computationally expensive. Enhanced sampling methods offer improvements but re...
Journal of agricultural and food chemistry
Nov 4, 2025
Gout is an inflammatory arthritis caused by urate crystal accumulation, and discovering natural xanthine oxidase (XO) inhibitors from food and agricultural sources is of growing interest. In this study, we employed AI-driven virtual screening to iden...
Journal of computer-aided molecular design
Nov 4, 2025
Evolution has optimized proteins over time by the incorporation of precise and context-specific amino acid substitutions adapted to structural and functional demands. We have reconceptualized this principle using deep learning to engineer monoclonal ...
Journal of agricultural and food chemistry
Nov 3, 2025
Traditional agricultural urease inhibitors encounter a low inhibition efficiency and a short duration of action. Therefore, the typical traditional urease inhibitor -butylthiophosphoric acid triamide (NBPT) was modified by molecular docking and molec...
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