[HTML][HTML] Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems

Q Mao, M Feng, XZ Jiang, Y Ren, KH Luo… - Progress in Energy and …, 2023 - Elsevier
Molecular dynamics (MD) has evolved into a ubiquitous, versatile and powerful
computational method for fundamental research in science branches such as biology …

[HTML][HTML] CADD, AI and ML in drug discovery: A comprehensive review

D Vemula, P Jayasurya, V Sushmitha, YN Kumar… - European Journal of …, 2023 - Elsevier
Computer-aided drug design (CADD) is an emerging field that has drawn a lot of interest
because of its potential to expedite and lower the cost of the drug development process …

Machine-learning methods for ligand–protein molecular docking

K Crampon, A Giorkallos, M Deldossi, S Baud… - Drug discovery today, 2022 - Elsevier
Artificial intelligence (AI) is often presented as a new Industrial Revolution. Many domains
use AI, including molecular simulation for drug discovery. In this review, we provide an …

Protein assembly by design

J Zhu, N Avakyan, A Kakkis, AM Hoffnagle… - Chemical …, 2021 - ACS Publications
Proteins are nature's primary building blocks for the construction of sophisticated molecular
machines and dynamic materials, ranging from protein complexes such as photosystem II …

Concepts of artificial intelligence for computer-assisted drug discovery

X Yang, Y Wang, R Byrne, G Schneider… - Chemical …, 2019 - ACS Publications
Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides
opportunities for the discovery and development of innovative drugs. Various machine …

PhysNet: A neural network for predicting energies, forces, dipole moments, and partial charges

OT Unke, M Meuwly - Journal of chemical theory and computation, 2019 - ACS Publications
In recent years, machine learning (ML) methods have become increasingly popular in
computational chemistry. After being trained on appropriate ab initio reference data, these …

Carbon nanodots from an in silico perspective

F Mocci, L de Villiers Engelbrecht, C Olla… - Chemical …, 2022 - ACS Publications
Carbon nanodots (CNDs) are the latest and most shining rising stars among
photoluminescent (PL) nanomaterials. These carbon-based surface-passivated …

Identification of bioactive molecules from tea plant as SARS-CoV-2 main protease inhibitors

VK Bhardwaj, R Singh, J Sharma… - Journal of …, 2021 - Taylor & Francis
The SARS-CoV-2 is the causative agent of COVID-19 pandemic that is causing a global
health emergency. The lack of targeted therapeutics and limited treatment options have …

Modeling and simulations of polymers: a roadmap

TE Gartner III, A Jayaraman - Macromolecules, 2019 - ACS Publications
Molecular modeling and simulations are invaluable tools for the polymer science and
engineering community. These computational approaches enable predictions and provide …

The Rosetta all-atom energy function for macromolecular modeling and design

RF Alford, A Leaver-Fay, JR Jeliazkov… - Journal of chemical …, 2017 - ACS Publications
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse
biological questions and engineering challenges ranging from interpretation of low …