Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening

J Kuan, M Radaeva, A Avenido… - Wiley …, 2023 - Wiley Online Library
Recent efforts to synthetically expand drug‐like chemical libraries have led to the
emergence of unprecedently large virtual databases. This surge of make‐on‐demand …

Data-driven design of polymer-based biomaterials: high-throughput simulation, experimentation, and machine learning

RA Patel, MA Webb - ACS Applied Bio Materials, 2023 - ACS Publications
Polymers, with the capacity to tunably alter properties and response based on manipulation
of their chemical characteristics, are attractive components in biomaterials. Nevertheless …

Sample efficiency matters: a benchmark for practical molecular optimization

W Gao, T Fu, J Sun, C Coley - Advances in neural …, 2022 - proceedings.neurips.cc
Molecular optimization is a fundamental goal in the chemical sciences and is of central
interest to drug and material design. In recent years, significant progress has been made in …

Geometric deep learning for structure-based ligand design

AS Powers, HH Yu, P Suriana, RV Koodli… - ACS Central …, 2023 - ACS Publications
A pervasive challenge in drug design is determining how to expand a ligand─ a small
molecule that binds to a target biomolecule─ in order to improve various properties of the …

GAUCHE: a library for Gaussian processes in chemistry

RR Griffiths, L Klarner, H Moss… - Advances in …, 2024 - proceedings.neurips.cc
We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry.
Gaussian processes have long been a cornerstone of probabilistic machine learning …

Calibration and generalizability of probabilistic models on low-data chemical datasets with DIONYSUS

G Tom, RJ Hickman, A Zinzuwadia, A Mohajeri… - Digital …, 2023 - pubs.rsc.org
Deep learning models that leverage large datasets are often the state of the art for modelling
molecular properties. When the datasets are smaller (< 2000 molecules), it is not clear that …

Streamlining large chemical library docking with artificial intelligence: the PyRMD2Dock approach

M Roggia, B Natale, G Amendola… - Journal of Chemical …, 2023 - ACS Publications
The present contribution introduces a novel computational protocol called PyRMD2Dock,
which combines the Ligand-Based Virtual Screening (LBVS) tool PyRMD with the popular …

Traversing chemical space with active deep learning for low-data drug discovery

D van Tilborg, F Grisoni - Nature Computational Science, 2024 - nature.com
Deep learning is accelerating drug discovery. However, current approaches are often
affected by limitations in the available data, in terms of either size or molecular diversity …

Pareto optimization to accelerate multi-objective virtual screening

JC Fromer, DE Graff, CW Coley - Digital Discovery, 2024 - pubs.rsc.org
The discovery of therapeutic molecules is fundamentally a multi-objective optimization
problem. One formulation of the problem is to identify molecules that simultaneously exhibit …

Driving school for self-driving labs

KL Snapp, KA Brown - Digital Discovery, 2023 - pubs.rsc.org
Self-driving labs (SDLs) have emerged as a strategy for accelerating materials and chemical
research. While such systems autonomously select and perform physical experiments, this …