Structure-based drug repurposing: Traditional and advanced AI/ML-aided methods
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 …
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
Graph neural network (GNN)-based deep learning (DL) models have been widely
implemented to predict the experimental aqueous solvation free energy, while its prediction …
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 …
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 …
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 …
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 …
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
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) …
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
Due to the limitation of solvent models, quantum chemistry calculation of solution-phase
molecular properties often deviates from experimental measurements. Recently, Δ-machine …
molecular properties often deviates from experimental measurements. Recently, Δ-machine …
Fragment quantum mechanical method for large-sized ion–water clusters
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 …
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 …
resistant vectors, insufficiently effective vaccines, and drugs that cannot stop parasitic …