Geometric deep learning for structure-based ligand design

AS Powers, HH Yu, P Suriana, RV Koodli… - ACS Central …, 2023 - ACS Publications
A pervasive challenge in drug design is determining how to expand a ligand─ a small
molecule that binds to a target biomolecule─ in order to improve various properties of the …

Fake it until you make it? generative de novo design and virtual screening of synthesizable molecules

M Stanley, M Segler - Current Opinion in Structural Biology, 2023 - Elsevier
Computational techniques, including virtual screening, de novo design, and generative
models, play an increasing role in expediting DMTA cycles for modern molecular discovery …

[HTML][HTML] Artificial intelligence and machine learning based intervention in medical infrastructure: a review and future trends

K Kumar, P Kumar, D Deb, ML Unguresan, V Muresan - Healthcare, 2023 - mdpi.com
People in the life sciences who work with Artificial Intelligence (AI) and Machine Learning
(ML) are under increased pressure to develop algorithms faster than ever. The possibility of …

[HTML][HTML] Current strategies in assessment of nanotoxicity: alternatives to in vivo animal testing

HJ Huang, YH Lee, YH Hsu, CT Liao, YF Lin… - International journal of …, 2021 - mdpi.com
Millions of experimental animals are widely used in the assessment of toxicological or
biological effects of manufactured nanomaterials in medical technology. However, the …

[HTML][HTML] DeepFrag: a deep convolutional neural network for fragment-based lead optimization

H Green, DR Koes, JD Durrant - Chemical Science, 2021 - pubs.rsc.org
Machine learning has been increasingly applied to the field of computer-aided drug
discovery in recent years, leading to notable advances in binding-affinity prediction, virtual …

The art and science of molecular docking

JM Paggi, A Pandit, RO Dror - Annual Review of Biochemistry, 2024 - annualreviews.org
Molecular docking has become an essential part of a structural biologist's and medicinal
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …

Docking-based generative approaches in the search for new drug candidates

T Danel, J Łęski, S Podlewska, IT Podolak - Drug Discovery Today, 2023 - Elsevier
Highlights•Compound enumeration coupled with docking is rapidly gaining
popularity.•Docking-based generative models are reviewed.•New taxonomy for docking …

[HTML][HTML] PARP1: Structural insights and pharmacological targets for inhibition

JO Spiegel, B Van Houten, JD Durrant - DNA repair, 2021 - Elsevier
Abstract Poly (ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a
multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair …

Comparative study of deep generative models on chemical space coverage

J Zhang, R Mercado, O Engkvist… - Journal of Chemical …, 2021 - ACS Publications
In recent years, deep molecular generative models have emerged as promising methods for
de novo molecular design. Thanks to the rapid advance of deep learning techniques, deep …

[HTML][HTML] Thermodynamic origins of two-component multiphase condensates of proteins

PY Chew, JA Joseph, R Collepardo-Guevara… - Chemical …, 2023 - pubs.rsc.org
Intracellular condensates are highly multi-component systems in which complex phase
behaviour can ensue, including the formation of architectures comprising multiple …