[HTML][HTML] 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 …

[HTML][HTML] 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 …

ChemCrow: Augmenting large-language models with chemistry tools

AM Bran, S Cox, O Schilter, C Baldassari… - arXiv preprint arXiv …, 2023 - arxiv.org
Over the last decades, excellent computational chemistry tools have been developed.
Integrating them into a single platform with enhanced accessibility could help reaching their …

AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings

J Eberhardt, D Santos-Martins… - Journal of chemical …, 2021 - ACS Publications
AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties

G Xiong, Z Wu, J Yi, L Fu, Z Yang, C Hsieh… - Nucleic acids …, 2021 - academic.oup.com
Because undesirable pharmacokinetics and toxicity of candidate compounds are the main
reasons for the failure of drug development, it has been widely recognized that absorption …

[HTML][HTML] Artificial intelligence–enabled virtual screening of ultra-large chemical libraries with deep docking

F Gentile, JC Yaacoub, J Gleave, M Fernandez… - Nature …, 2022 - nature.com
With the recent explosion of chemical libraries beyond a billion molecules, more efficient
virtual screening approaches are needed. The Deep Docking (DD) platform enables up to …

A review of molecular representation in the age of machine learning

DS Wigh, JM Goodman… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
Research in chemistry increasingly requires interdisciplinary work prompted by, among
other things, advances in computing, machine learning, and artificial intelligence. Everyone …

[HTML][HTML] Augmenting large language models with chemistry tools

A M. Bran, S Cox, O Schilter, C Baldassari… - Nature Machine …, 2024 - nature.com
Large language models (LLMs) have shown strong performance in tasks across domains
but struggle with chemistry-related problems. These models also lack access to external …

Use of molecular docking computational tools in drug discovery

F Stanzione, I Giangreco, JC Cole - Progress in Medicinal Chemistry, 2021 - Elsevier
Molecular docking has become an important component of the drug discovery process.
Since first being developed in the 1980s, advancements in the power of computer hardware …

Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor

EA Fink, J Xu, H Hübner, JM Braz, P Seemann, C Avet… - Science, 2022 - science.org
Because nonopioid analgesics are much sought after, we computationally docked more
than 301 million virtual molecules against a validated pain target, the α2A-adrenergic …