Uncertainty quantification in drug design

LH Mervin, S Johansson, E Semenova, KA Giblin… - Drug discovery today, 2021 - Elsevier
Highlights•Review of the state-of-the-art in uncertainty quantification in drug
design.•Examples from drug-design settings are provided.•Impact on decision making is …

[HTML][HTML] Computational analyses of mechanism of action (MoA): data, methods and integration

MA Trapotsi, L Hosseini-Gerami, A Bender - RSC Chemical Biology, 2022 - pubs.rsc.org
The elucidation of a compound's Mechanism of Action (MoA) is a challenging task in the
drug discovery process, but it is important in order to rationalise phenotypic findings and to …

Multispecies machine learning predictions of in vitro intrinsic clearance with uncertainty quantification analyses

R Rodríguez-Pérez, M Trunzer… - Molecular …, 2022 - ACS Publications
In pharmaceutical research, compounds are optimized for metabolic stability to avoid a too
fast elimination of the drug. Intrinsic clearance (CLint) measured in liver microsomes or …

[HTML][HTML] A universal similarity based approach for predictive uncertainty quantification in materials science

V Korolev, I Nevolin, P Protsenko - Scientific Reports, 2022 - nature.com
Immense effort has been exerted in the materials informatics community towards enhancing
the accuracy of machine learning (ML) models; however, the uncertainty quantification (UQ) …

Applications of artificial intelligence in drug design: opportunities and challenges

M Thomas, A Boardman, M Garcia-Ortegon… - Artificial Intelligence in …, 2022 - Springer
Artificial intelligence (AI) has undergone rapid development in recent years and has been
successfully applied to real-world problems such as drug design. In this chapter, we review …

Comparison of chemical structure and cell morphology information for multitask bioactivity predictions

MA Trapotsi, LH Mervin, AM Afzal, N Sturm… - Journal of chemical …, 2021 - ACS Publications
The understanding of the mechanism-of-action (MoA) of compounds and the prediction of
potential drug targets play an important role in small-molecule drug discovery. The aim of …

[PDF][PDF] Uncertainty quantification: Can we trust artificial intelligence in drug discovery?

J Yu, D Wang, M Zheng - Iscience, 2022 - cell.com
The problem of human trust is one of the most fundamental problems in applied artificial
intelligence in drug discovery. In silico models have been widely used to accelerate the …

[HTML][HTML] Testing the predictive power of reverse screening to infer drug targets, with the help of machine learning

A Daina, V Zoete - Communications Chemistry, 2024 - nature.com
Estimating protein targets of compounds based on the similarity principle—similar molecules
are likely to show comparable bioactivity—is a long-standing strategy in drug research …

[HTML][HTML] Probabilistic Random Forest improves bioactivity predictions close to the classification threshold by taking into account experimental uncertainty

LH Mervin, MA Trapotsi, AM Afzal, IP Barrett… - Journal of …, 2021 - Springer
Measurements of protein–ligand interactions have reproducibility limits due to experimental
errors. Any model based on such assays will consequentially have such unavoidable errors …

Large-Scale Screening for High Conductivity Ionic Liquids via Machine Learning Algorithm Utilizing Graph Neural Network-Based Features

C Song, C Wang, F Fang, G Zhou, Z Dai… - Journal of Chemical & …, 2024 - ACS Publications
Ionic conductivity is a crucial parameter in the electrochemical applications of ionic liquids
(ILs). Conventional methods to obtain this parameter, ie, experimental measurements or …