Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations
J Chen, X Wang, L Pang, JZH Zhang… - Nucleic Acids …, 2019 - academic.oup.com
Riboswitches can regulate gene expression by direct and specific interactions with ligands
and have recently attracted interest as potential drug targets for antibacterial. In this work …
and have recently attracted interest as potential drug targets for antibacterial. In this work …
Explainable supervised machine learning model to predict solvation gibbs energy
J Ferraz-Caetano, F Teixeira… - Journal of Chemical …, 2023 - ACS Publications
Many challenges persist in developing accurate computational models for predicting
solvation free energy (Δ G sol). Despite recent developments in Machine Learning (ML) …
solvation free energy (Δ G sol). Despite recent developments in Machine Learning (ML) …
Computing converged free energy differences between levels of theory via nonequilibrium work methods: Challenges and opportunities
FL Kearns, PS Hudson, HL Woodcock… - Journal of …, 2017 - Wiley Online Library
We demonstrate that Jarzynski's equation can be used to reliably compute free energy
differences between low and high level representations of systems. The need for such a …
differences between low and high level representations of systems. The need for such a …
Development of a robust indirect approach for MM→ QM free energy calculations that combines force-matched reference potential and Bennett's acceptance ratio …
TJ Giese, DM York - Journal of chemical theory and computation, 2019 - ACS Publications
We use the PBE0/6-31G* density functional method to perform ab initio quantum
mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under …
mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under …
Molecular mechanism of binding selectivity of inhibitors toward BACE1 and BACE2 revealed by multiple short molecular dynamics simulations and free-energy …
J Chen, J Wang, B Yin, L Pang, W Wang… - ACS Chemical …, 2019 - ACS Publications
The β-amyloid cleaving enzymes 1 and 2 (BACE1 and BACE2) have been regarded as the
prospective targets for clinically treating Alzheimer's disease (AD) in the last two decades …
prospective targets for clinically treating Alzheimer's disease (AD) in the last two decades …
Perspective: Reference-Potential Methods for the Study of Thermodynamic Properties in Chemical Processes: Theory, Applications, and Pitfalls
In silico investigations of enzymatic reactions and chemical reactions in condensed phases
often suffer from formidable computational costs due to a large number of degrees of …
often suffer from formidable computational costs due to a large number of degrees of …
Binding of inhibitors to BACE1 affected by pH-dependent protonation: An exploration from multiple replica Gaussian accelerated molecular dynamics and MM-GBSA …
J Chen, S Zhang, W Wang, H Sun… - ACS Chemical …, 2021 - ACS Publications
To date, inhibiting the activity of β-amyloid cleaving enzyme 1 (BACE1) has been
considered an efficient approach for treating Alzheimer's disease (AD). In the current work …
considered an efficient approach for treating Alzheimer's disease (AD). In the current work …
Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy …
TS Hofer, PH Hünenberger - The Journal of chemical physics, 2018 - pubs.aip.org
Absolute proton hydration free energy, surface potential of water, and redox potential of the
hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and …
hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and …
Binding selectivity-dependent molecular mechanism of inhibitors towards CDK2 and CDK6 investigated by multiple short molecular dynamics and free energy …
L Wang, D Lu, Y Wang, X Xu, P Zhong… - Journal of Enzyme …, 2023 - Taylor & Francis
Understanding selectivity-dependent molecular mechanism of inhibitors towards CDK2 over
CDK6 is prominent for improving drug design towards the CDK family. Multiple short …
CDK6 is prominent for improving drug design towards the CDK family. Multiple short …
Molecular mechanism with regard to the binding selectivity of inhibitors toward FABP5 and FABP7 explored by multiple short molecular dynamics simulations and free …
J Chen, X Liu, S Zhang, J Chen, H Sun… - Physical Chemistry …, 2020 - pubs.rsc.org
Recently, fatty acid binding proteins 5 and 7 (FABP5 and FABP7) have been regarded as
the prospective targets for clinically treating multiple diseases related to FABPs. In this work …
the prospective targets for clinically treating multiple diseases related to FABPs. In this work …