The journal of physical chemistry letters
Nov 11, 2022
Nonadiabatic coupling (NAC) plays a central role in driving nonadiabatic dynamics in various photophysical and photochemical processes. However, the high computational cost of NAC limits the time scale and system size of quantum dynamics simulation. ...
More than 7000 per- and polyfluorinated alkyl substances (PFAS) have been documented in the U.S. Environmental Protection Agency's CompTox Chemicals database. These PFAS can be used in a broad range of industrial and consumer applications but may pos...
A fundamental question in protein science is where allosteric hotspots - residues critical for allosteric signaling - are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allo...
In the recent COVID-19 pandemic, SARS-CoV-2 infection spread worldwide. The 3C-like protease (3CLpro) is a promising drug target for SARS-CoV-2. We constructed a deep learning-based convolutional neural network-quantitative structure-activity relat...
Journal of chemical theory and computation
Sep 27, 2022
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromopho...
Proceedings of the National Academy of Sciences of the United States of America
Sep 26, 2022
Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing col...
Journal of chemical information and modeling
Sep 13, 2022
The availability of AlphaFold2 has led to great excitement in the scientific community─particularly among drug hunters─due to the ability of the algorithm to predict protein structures with high accuracy. However, beyond globally accurate protein str...
Journal of chemical theory and computation
Sep 8, 2022
Sampling the minimum energy path (MEP) between two minima of a system is often hindered by the presence of an energy barrier separating the two metastable states. As a consequence, direct sampling based on molecular dynamics or Markov Chain Monte Car...
Journal of chemical information and modeling
Sep 6, 2022
Among the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water site distribution function around the protein, is crucial. The typical methods for computing the...
The outbreak of COVID-19 caused millions of deaths worldwide, and the number of total infections is still rising. It is necessary to identify some potentially effective drugs that can be used to prevent the development of severe symptoms, or even dea...