Structure-based drug repurposing: Traditional and advanced AI/ML-aided methods

C Choudhury, NA Murugan, UD Priyakumar - Drug discovery today, 2022 - Elsevier
Highlights•Repurposing existing drugs for new diseases is cost effective and time saving.•In
silico methods are crucial for rapid drug screening in the early stages.•Machine learning …

Accurate prediction of aqueous free solvation energies using 3D atomic feature-based graph neural network with transfer learning

D Zhang, S Xia, Y Zhang - Journal of chemical information and …, 2022 - ACS Publications
Graph neural network (GNN)-based deep learning (DL) models have been widely
implemented to predict the experimental aqueous solvation free energy, while its prediction …

Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems

J Liu, X He - Wiley Interdisciplinary Reviews: Computational …, 2023 - Wiley Online Library
Quantum mechanical (QM) calculations are critical in quantitatively understanding the
relationship between the structure and physicochemical properties of various chemical …

Protein–ligand interaction energies from quantum-chemical fragmentation methods: Upgrading the MFCC-scheme with many-body contributions

JR Vornweg, CR Jacob - The Journal of Physical Chemistry B, 2024 - ACS Publications
Quantum-chemical fragmentation methods offer an attractive approach for the accurate
calculation of protein–ligand interaction energies. While the molecular fractionation with …

Computational studies of protein–drug binding affinity changes upon mutations in the drug target

R Friedman - Wiley Interdisciplinary Reviews: Computational …, 2022 - Wiley Online Library
Mutations that lead to drug resistance limit the efficacy of antibiotics, antiviral drugs, targeted
cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity …

In silico evaluation of the binding energies of androgen receptor agonists in wild-type and mutational models

ACC Albuquerque, KS Bezerra… - The Journal of …, 2023 - ACS Publications
Anabolic androgenic steroids (AAS) are substances with androgenic and anabolic
characteristics. Among the many side effects of hormone therapy with AAS, the following …

Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids

J Liu, X He - Physical Chemistry Chemical Physics, 2020 - pubs.rsc.org
To study large molecular systems beyond the system size that the current state-of-the-art ab
initio electronic structure methods could handle, fragment-based quantum mechanical (QM) …

Δ-Machine learning for quantum chemistry prediction of solution-phase molecular properties at the ground and excited states

X Chen, P Li, E Hruska, F Liu - Physical Chemistry Chemical Physics, 2023 - pubs.rsc.org
Due to the limitation of solvent models, quantum chemistry calculation of solution-phase
molecular properties often deviates from experimental measurements. Recently, Δ-machine …

Fragment quantum mechanical method for large-sized ion–water clusters

J Liu, LW Qi, JZH Zhang, X He - Journal of chemical theory and …, 2017 - ACS Publications
Fragmentation methods have been widely studied for computing quantum mechanical (QM)
energy of medium-sized water clusters, but less attention has been paid to large-sized ion …

Deciphering Interactions between Potential Inhibitors and the Plasmodium falciparum DHODH Enzyme: A Computational Perspective

AH Lima Costa, KS Bezerra… - The Journal of …, 2023 - ACS Publications
Malaria is a parasitic disease that, in its most severe form, can even lead to death. Insect-
resistant vectors, insufficiently effective vaccines, and drugs that cannot stop parasitic …