Computational approaches streamlining drug discovery

AV Sadybekov, V Katritch - Nature, 2023 - nature.com
Computer-aided drug discovery has been around for decades, although the past few years
have seen a tectonic shift towards embracing computational technologies in both academia …

Molecular docking: principles, advances, and its applications in drug discovery

MT Muhammed, E Aki-Yalcin - Letters in Drug Design & …, 2024 - benthamdirect.com
Molecular docking is a structure-based computational method that generates the binding
pose and affinity between ligands and targets. There are many powerful docking programs …

Contrastive learning in protein language space predicts interactions between drugs and protein targets

R Singh, S Sledzieski, B Bryson… - Proceedings of the …, 2023 - National Acad Sciences
Sequence-based prediction of drug–target interactions has the potential to accelerate drug
discovery by complementing experimental screens. Such computational prediction needs to …

Boosting protein–ligand binding pose prediction and virtual screening based on residue–atom distance likelihood potential and graph transformer

C Shen, X Zhang, Y Deng, J Gao, D Wang… - Journal of Medicinal …, 2022 - ACS Publications
The past few years have witnessed enormous progress toward applying machine learning
approaches to the development of protein–ligand scoring functions. However, the robust …

Application of computational biology and artificial intelligence in drug design

Y Zhang, M Luo, P Wu, S Wu, TY Lee, C Bai - International journal of …, 2022 - mdpi.com
Traditional drug design requires a great amount of research time and developmental
expense. Booming computational approaches, including computational biology, computer …

[HTML][HTML] A guide to in silico drug design

Y Chang, BA Hawkins, JJ Du, PW Groundwater… - Pharmaceutics, 2023 - mdpi.com
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …

Evaluation of AlphaFold2 structures as docking targets

M Holcomb, YT Chang, DS Goodsell, S Forli - Protein Science, 2023 - Wiley Online Library
AlphaFold2 is a promising new tool for researchers to predict protein structures and
generate high‐quality models, with low backbone and global root‐mean‐square deviation …

A generalized protein–ligand scoring framework with balanced scoring, docking, ranking and screening powers

C Shen, X Zhang, CY Hsieh, Y Deng, D Wang, L Xu… - Chemical …, 2023 - pubs.rsc.org
Applying machine learning algorithms to protein–ligand scoring functions has aroused
widespread attention in recent years due to the high predictive accuracy and affordable …

DrugRep: an automatic virtual screening server for drug repurposing

J Gan, J Liu, Y Liu, S Chen, W Dai, ZX **ao… - Acta Pharmacologica …, 2023 - nature.com
Computationally identifying new targets for existing drugs has drawn much attention in drug
repurposing due to its advantages over de novo drugs, including low risk, low costs, and …

From traditional ethnopharmacology to modern natural drug discovery: A methodology discussion and specific examples

S Pirintsos, A Panagiotopoulos, M Bariotakis… - Molecules, 2022 - mdpi.com
Ethnopharmacology, through the description of the beneficial effects of plants, has provided
an early framework for the therapeutic use of natural compounds. Natural products, either in …