Applying Classical, Ab Initio, and Machine-Learning Molecular Dynamics Simulations to the Liquid Electrolyte for Rechargeable Batteries

N Yao, X Chen, ZH Fu, Q Zhang - Chemical Reviews, 2022 - ACS Publications
Rechargeable batteries have become indispensable implements in our daily life and are
considered a promising technology to construct sustainable energy systems in the future …

Two decades of Martini: Better beads, broader scope

SJ Marrink, L Monticelli, MN Melo… - Wiley …, 2023 - Wiley Online Library
The Martini model, a coarse‐grained force field for molecular dynamics simulations, has
been around for nearly two decades. Originally developed for lipid‐based systems by the …

Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides

A Vidal-Limon, JE Aguilar-Toalá… - Journal of agricultural …, 2022 - ACS Publications
In silico tools, such as molecular docking, are widely applied to study interactions and
binding affinity of biological activity of proteins and peptides. However, restricted sampling of …

Advances in protein structure prediction and design

B Kuhlman, P Bradley - Nature reviews molecular cell biology, 2019 - nature.com
The prediction of protein three-dimensional structure from amino acid sequence has been a
grand challenge problem in computational biophysics for decades, owing to its intrinsic …

AlphaFold, artificial intelligence (AI), and allostery

R Nussinov, M Zhang, Y Liu, H Jang - The Journal of Physical …, 2022 - ACS Publications
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of
biological sequence data and artificial intelligence (AI). AlphaFold has appended projects …

The coming of age of AI/ML in drug discovery, development, clinical testing, and manufacturing: the FDA perspectives

SK Niazi - Drug Design, Development and Therapy, 2023 - Taylor & Francis
Artificial intelligence (AI) and machine learning (ML) represent significant advancements in
computing, building on technologies that humanity has developed over millions of years …

Machine learning coarse-grained potentials of protein thermodynamics

M Majewski, A Pérez, P Thölke, S Doerr… - Nature …, 2023 - nature.com
A generalized understanding of protein dynamics is an unsolved scientific problem, the
solution of which is critical to the interpretation of the structure-function relationships that …

Quantitative magnetic resonance imaging of brain anatomy and in vivo histology

N Weiskopf, LJ Edwards, G Helms… - Nature Reviews …, 2021 - nature.com
Quantitative magnetic resonance imaging (qMRI) goes beyond conventional MRI, which
aims primarily at local image contrast. It provides specific physical parameters related to the …

[HTML][HTML] Deep learning methods in protein structure prediction

M Torrisi, G Pollastri, Q Le - Computational and structural biotechnology …, 2020 - Elsevier
Abstract Protein Structure Prediction is a central topic in Structural Bioinformatics. Since
the'60s statistical methods, followed by increasingly complex Machine Learning and recently …

Coarse-grained protein models and their applications

S Kmiecik, D Gront, M Kolinski, L Wieteska… - Chemical …, 2016 - ACS Publications
The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …