Drug discovery with explainable artificial intelligence

J Jiménez-Luna, F Grisoni, G Schneider - Nature Machine Intelligence, 2020 - nature.com
Deep learning bears promise for drug discovery, including advanced image analysis,
prediction of molecular structure and function, and automated generation of innovative …

Big-data science in porous materials: materials genomics and machine learning

KM Jablonka, D Ongari, SM Moosavi, B Smit - Chemical reviews, 2020 - ACS Publications
By combining metal nodes with organic linkers we can potentially synthesize millions of
possible metal–organic frameworks (MOFs). The fact that we have so many materials opens …

Data‐Driven Materials Innovation and Applications

Z Wang, Z Sun, H Yin, X Liu, J Wang, H Zhao… - Advanced …, 2022 - Wiley Online Library
Owing to the rapid developments to improve the accuracy and efficiency of both
experimental and computational investigative methodologies, the massive amounts of data …

Software tools and approaches for compound identification of LC-MS/MS data in metabolomics

I Blaženović, T Kind, J Ji, O Fiehn - Metabolites, 2018 - mdpi.com
The annotation of small molecules remains a major challenge in untargeted mass
spectrometry-based metabolomics. We here critically discuss structured elucidation …

A practical guide to machine-learning scoring for structure-based virtual screening

VK Tran-Nguyen, M Junaid, S Simeon, PJ Ballester - Nature Protocols, 2023 - nature.com
Abstract Structure-based virtual screening (SBVS) via docking has been used to discover
active molecules for a range of therapeutic targets. Chemical and protein data sets that …

Principles of QSAR modeling: comments and suggestions from personal experience

P Gramatica - International Journal of Quantitative Structure-Property …, 2020 - igi-global.com
At the end of her academic career, the author summarizes the main aspects of QSAR
modeling, giving comments and suggestions according to her 23 years' experience in QSAR …

OPERA models for predicting physicochemical properties and environmental fate endpoints

K Mansouri, CM Grulke, RS Judson… - Journal of …, 2018 - Springer
The collection of chemical structure information and associated experimental data for
quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by …

Converting nanotoxicity data to information using artificial intelligence and simulation

X Yan, T Yue, DA Winkler, Y Yin, H Zhu… - Chemical …, 2023 - ACS Publications
Decades of nanotoxicology research have generated extensive and diverse data sets.
However, data is not equal to information. The question is how to extract critical information …

Leveraging molecular structure and bioactivity with chemical language models for de novo drug design

M Moret, I Pachon Angona, L Cotos, S Yan… - Nature …, 2023 - nature.com
Generative chemical language models (CLMs) can be used for de novo molecular structure
generation by learning from a textual representation of molecules. Here, we show that hybrid …

iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach

A Daina, O Michielin, V Zoete - Journal of chemical information …, 2014 - ACS Publications
The n-octanol/water partition coefficient (log P o/w) is a key physicochemical parameter for
drug discovery, design, and development. Here, we present a physics-based approach that …