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 …

Integrating QSAR modelling and deep learning in drug discovery: the emergence of deep QSAR

A Tropsha, O Isayev, A Varnek, G Schneider… - Nature Reviews Drug …, 2024 - nature.com
Quantitative structure–activity relationship (QSAR) modelling, an approach that was
introduced 60 years ago, is widely used in computer-aided drug design. In recent years …

The neural basis of psychedelic action

AC Kwan, DE Olson, KH Preller, BL Roth - Nature Neuroscience, 2022 - nature.com
Psychedelics are serotonin 2A receptor agonists that can lead to profound changes in
perception, cognition and mood. In this review, we focus on the basic neurobiology …

Machine learning-aided generative molecular design

Y Du, AR Jamasb, J Guo, T Fu, C Harris… - Nature Machine …, 2024 - nature.com
Abstract Machine learning has provided a means to accelerate early-stage drug discovery
by combining molecule generation and filtering steps in a single architecture that leverages …

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 …

Bespoke library docking for 5-HT2A receptor agonists with antidepressant activity

AL Kaplan, DN Confair, K Kim, X Barros-Álvarez… - Nature, 2022 - nature.com
There is considerable interest in screening ultralarge chemical libraries for ligand discovery,
both empirically and computationally,,–. Efforts have focused on readily synthesizable …

Rings in clinical trials and drugs: present and future

J Shearer, JL Castro, ADG Lawson… - Journal of medicinal …, 2022 - ACS Publications
We present a comprehensive analysis of all ring systems (both heterocyclic and
nonheterocyclic) in clinical trial compounds and FDA-approved drugs. We show 67% of …

The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods

B Zdrazil, E Felix, F Hunter, EJ Manners… - Nucleic acids …, 2024 - academic.oup.com
Abstract ChEMBL (https://www. ebi. ac. uk/chembl/) is a manually curated, high-quality, large-
scale, open, FAIR and Global Core Biodata Resource of bioactive molecules with drug-like …

Epik: pKa and Protonation State Prediction through Machine Learning

RC Johnston, K Yao, Z Kaplan, M Chelliah… - Journal of chemical …, 2023 - ACS Publications
Epik version 7 is a software program that uses machine learning for predicting the p K a
values and protonation state distribution of complex, druglike molecules. Using an ensemble …

A practical guide to large-scale docking

BJ Bender, S Gahbauer, A Luttens, J Lyu, CM Webb… - Nature protocols, 2021 - nature.com
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …