Modeling the expansion of virtual screening libraries

J Lyu, JJ Irwin, BK Shoichet - Nature Chemical Biology, 2023 - nature.com
Recently,'tangible'virtual libraries have made billions of molecules readily available.
Prioritizing these molecules for synthesis and testing demands computational approaches …

Accelerating high-throughput virtual screening through molecular pool-based active learning

DE Graff, EI Shakhnovich, CW Coley - Chemical science, 2021 - pubs.rsc.org
Structure-based virtual screening is an important tool in early stage drug discovery that
scores the interactions between a target protein and candidate ligands. As virtual libraries …

Synthon-based ligand discovery in virtual libraries of over 11 billion compounds

AA Sadybekov, AV Sadybekov, Y Liu… - Nature, 2022 - nature.com
Abstract Structure-based virtual ligand screening is emerging as a key paradigm for early
drug discovery owing to the availability of high-resolution target structures,,–and ultra-large …

A geometric deep learning approach to predict binding conformations of bioactive molecules

O Méndez-Lucio, M Ahmad… - Nature Machine …, 2021 - nature.com
Understanding the interactions formed between a ligand and its molecular target is key to
guiding the optimization of molecules. Different experimental and computational methods …

Structure-based virtual screening for ligands of G protein–coupled receptors: what can molecular docking do for you?

F Ballante, AJ Kooistra, S Kampen, C de Graaf… - Pharmacological …, 2021 - ASPET
G protein–coupled receptors (GPCRs) constitute the largest family of membrane proteins in
the human genome and are important therapeutic targets. During the last decade, the …

Improving protein-ligand docking results with high-throughput molecular dynamics simulations

H Guterres, W Im - Journal of Chemical Information and Modeling, 2020 - ACS Publications
Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …

Autonomous discovery in the chemical sciences part I: Progress

CW Coley, NS Eyke, KF Jensen - … Chemie International Edition, 2020 - Wiley Online Library
This two‐part Review examines how automation has contributed to different aspects of
discovery in the chemical sciences. In this first part, we describe a classification for …

Accelerating bayesian optimization for biological sequence design with denoising autoencoders

S Stanton, W Maddox, N Gruver… - International …, 2022 - proceedings.mlr.press
Bayesian optimization (BayesOpt) is a gold standard for query-efficient continuous
optimization. However, its adoption for drug design has been hindered by the discrete, high …

Graph neural networks for automated de novo drug design

J Xiong, Z Xiong, K Chen, H Jiang, M Zheng - Drug discovery today, 2021 - Elsevier
Highlights•GNN has attracted wide attention from the field of designing drug molecules.•The
applications of GNN in molecule scoring, molecule generation and optimization, and …

The synthesizability of molecules proposed by generative models

W Gao, CW Coley - Journal of chemical information and modeling, 2020 - ACS Publications
The discovery of functional molecules is an expensive and time-consuming process,
exemplified by the rising costs of small molecule therapeutic discovery. One class of …