Yinglong Miao

Apr 15, 2024 | dx.doi.org | Jinan Wang |Yinglong Miao

Binding thermodynamics and kinetics play critical roles in drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics of small molecules and flexible peptides using conventional molecular dynamics (cMD), due to limited simulation time scales.

Dec 27, 2023 | mdpi.com | Yinglong Miao |Victor A. Adediwura

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Sep 28, 2023 | biorxiv.org | Hung N Do |Shweta R Malvankar |Michael Wolfe |Yinglong Miao

Abstractγ-Secretase is an intramembrane aspartyl protease complex which cleaves the transmembrane domain of over 150 peptide substrates, including amyloid precursor protein (APP) and the Notch family of receptors, via two conserved aspartates D257 and D385 in the Presenilin-1 (PS1) catalytic subunit. However, while the activation of γ-secretase for cleavage of APP has been widely studied, the cleavage of Notch by γ-secretase remains poorly explored.

Aug 10, 2023 | nature.com | Guoqing Xiang |Hung Nguyen Do |Joshua Levitz |Yinglong Miao

Abstractα1-adrenergic receptors (α1-ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists for all α1 subtypes has limited our understanding of the physiological roles of different α1-AR subtypes, and led to the stagnancy in agonist-based drug development for these receptors.

Apr 5, 2023 | biorxiv.org | Hung Nguyen Do |Yinglong Miao

AbstractWe have developed a new Deep Boosted Molecular Dynamics (DBMD) method. Probabilistic Bayesian neural network models were implemented to construct boost potentials that exhibit Gaussian distribution with minimized anharmonicity, thereby allowing for accurate energetic reweighting and enhanced sampling of molecular simulations. DBMD was demonstrated on model systems of alanine dipeptide and the fast-folding protein and RNA structures.