Julie Harris & Ruibin Liu, JCTC, 2022
We present the first CUDA implementation of the all-atom PME CpHMD method in Amber22.
Passion. Dedication. Hard work. Congratulations, Aarion! What a great start of the 4th year of PhD study!
Romany et al, Chem Mater, 2023
De novo self assembly simulations of chitin revealed the mechanism of inverse temperature dependence and polymorphism.
Liu et al, J Chem Inf Model, 2023
Low-cost quantum descriptors can predict the SAR of Michael acceptor warheads.
Romany et al, J Chem Inf Model, 2023
We identified druggable cysteines using a novel protocol that combines CpHMD and structural analysis.
Clayton & Oliverira et al, JCIM, 2023
The drug resistance mechanism of a SARS-CoV-2 Mpro mutant revealed using simulations, AI, & experiments.
Liu et al, RSC Med Chem, 2021
We assessed and rationalized the cysteine reactivities for all 14 MAP kinases.
Liu & Zhan et al, J Med Chem, 2021
Exploring the reactivities of the front pocket cysteine in human kinases for covalent drug design.
Mahinthichaichan et al, JACS Au 2021
We elucidated the mechanism and kinetics of fentanyl-mOR dissociation to help evaluate drug overdose reversal strategies.
Vo et al, Nat Commun 2021
Deciphering how fentanyl binds mu-opioid receptor represents the first step in understanding the cascade of molecular events leading to addiction.
Verma et al, J Am Chem Soc 2020.
Study of SARS main proteases revealed proton-coupled mechanism and an opportunity for small-molecule broad-spectrum antiviral drug design
Henderson et al, Proc Natl Acad Sci 2020.
Alternative binding site and proton sharing may represent important general mechanisms of proton-coupled transport in secondary active transporters
Harris et al, J Chem Theory Comput 2020.
Benchmarking our GPU-based CpHMD tool to facilitate targeted covalent inhibitor design
Mahinthichaichan et al, ACS Omega 2020.
Discover how electric signals induce conformational changes of an aminopolysaccharide chain in an unexpected way
Tsai et al, J Am Chem Soc 2019.
Allowing protonation states to change may be a key to sample the various conformational states of kinases.
Liu et al, J Am Chem Soc 2019.
A molecular dynamics tool put to test for discovering covalent hotspots in kinases and other drug targets.
Harris et al, J Chem Inf Model 2019.
A new GPU implementation for rapid and accurate pKa predictions and proton-coupled dynamics.
Tsai et al, Chem Mater 2018.
Exploiting a pKa gradient for persistent but erasable gradient in structural and mechanical properties.
Henderson et al, J Phys Chem Lett 2018.
Pyrimidine protonation shifts the ligand binding mode from water-mediated to direct hydrogen bonding.