Dielectric continuum methods for quantum chemistry
JM Herbert - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
This review describes the theory and implementation of implicit solvation models based on
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study
J Wang - Journal of chemical information and modeling, 2020 - ACS Publications
The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes
possible treatment strategies using drugs on the market. It is very efficient to apply computer …
possible treatment strategies using drugs on the market. It is very efficient to apply computer …
Recent developments in free energy calculations for drug discovery
The grand challenge in structure-based drug design is achieving accurate prediction of
binding free energies. Molecular dynamics (MD) simulations enable modeling of …
binding free energies. Molecular dynamics (MD) simulations enable modeling of …
Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics …
F Mosquera-Yuqui, N Lopez-Guerra… - Journal of …, 2022 - Taylor & Francis
Given the highly contagious nature of SARS-CoV-2, it has resulted in an unprecedented
number of COVID-19 infected and dead people worldwide. Since there is currently no …
number of COVID-19 infected and dead people worldwide. Since there is currently no …
Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout.
This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used …
This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used …
Improving the performance of MM/PBSA in protein–protein interactions via the screening electrostatic energy
Y Sheng, Y Yin, Y Ma, H Ding - Journal of Chemical Information …, 2021 - ACS Publications
Accurate calculation of protein–protein binding free energy is of great importance in
biological and medical science, yet it remains a hugely challenging problem. In this work, we …
biological and medical science, yet it remains a hugely challenging problem. In this work, we …
Can molecular dynamics simulations improve predictions of protein-ligand binding affinity with machine learning?
Binding affinity prediction largely determines the discovery efficiency of lead compounds in
drug discovery. Recently, machine learning (ML)-based approaches have attracted much …
drug discovery. Recently, machine learning (ML)-based approaches have attracted much …
Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses
Protein mutations occur frequently in biological systems, which may impact, for example, the
binding of drugs to their targets through impairing the critical H-bonds, changing the …
binding of drugs to their targets through impairing the critical H-bonds, changing the …
VAD-MM/GBSA: a variable atomic dielectric MM/GBSA model for improved accuracy in protein–ligand binding free energy calculations
The molecular mechanics/generalized Born surface area (MM/GBSA) has been widely used
in end-point binding free energy prediction in structure-based drug design (SBDD) …
in end-point binding free energy prediction in structure-based drug design (SBDD) …
[HTML][HTML] Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6
X Li, C Wang, T Peng, Z Chai, D Ni, Y Liu… - Computational and …, 2021 - Elsevier
CRISPR-Cas systems are prokaryotic adaptive immunity against invading phages and
plasmids. Phages have evolved diverse protein inhibitors of CRISPR-Cas systems, called …
plasmids. Phages have evolved diverse protein inhibitors of CRISPR-Cas systems, called …