Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions tha...
Electrostatics is of paramount importance to chemistry, physics, biology, and medicine. The Poisson-Boltzmann (PB) theory is a primary model for electrostatic analysis. However, it is highly challenging to compute accurate PB electrostatic solvation ...
Journal of chemical information and modeling
38757521
The atomic partial charge is of great importance in many fields, such as chemistry and drug-target recognition. However, conventional quantum-based computing of atomic charges is relatively slow, limiting further applications of atomic charge analysi...
Journal of chemical theory and computation
38888427
Accurately describing long-range interactions is a significant challenge in molecular dynamics (MD) simulations of proteins. High-quality long-range potential is also an important component of the range-separated machine learning force field. This st...
Nifedipine (NIF) is a dihydropyridine calcium channel blocker primarily used to treat conditions such as hypertension and angina. However, its low solubility and low bioavailability limit its effectiveness in clinical practice. Here, we developed a c...
Journal of chemical theory and computation
39504303
Intrinsically disordered proteins and regions (IDPs) are involved in vital biological processes. To understand the IDP function, often controlled by conformation, we need to find the link between sequence and conformation. We decode this link by inte...
Journal of chemical information and modeling
39469831
The ability to predict the strength of halogen bonds and properties of halogen bond (XB) donors has significant utility for medicinal chemistry and materials science. XBs are typically calculated through expensive ab initio methods. Thus, the develop...
Robotic artificial muscles, inspired by the adaptability of biological muscles, outperform rigid robots in dynamic environments due to their flexibility. However, the intrinsic compliance of the soft actuators restricts force transmission capacity an...
Journal of chemical information and modeling
39928564
Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes reve...
Journal of chemical theory and computation
40273117
Accurately modeling enzyme reactions through direct machine learning/molecular mechanics simulations remains challenging in describing the electrostatic coupling between the QM and MM subsystems. In this work, we proposed a reweighting ME (mechanic e...