Machine learning for electrocatalyst and photocatalyst design and discovery

H Mai, TC Le, D Chen, DA Winkler… - Chemical …, 2022 - ACS Publications
Electrocatalysts and photocatalysts are key to a sustainable future, generating clean fuels,
reducing the impact of global warming, and providing solutions to environmental pollution …

Graph neural networks for materials science and chemistry

P Reiser, M Neubert, A Eberhard, L Torresi… - Communications …, 2022 - nature.com
Abstract Machine learning plays an increasingly important role in many areas of chemistry
and materials science, being used to predict materials properties, accelerate simulations …

CB-Dock2: Improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting

Y Liu, X Yang, J Gan, S Chen, ZX Xiao… - Nucleic acids …, 2022 - academic.oup.com
Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors
and the corresponding binding poses of ligands. It has seen wide applications in …

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

R Krishna, J Wang, W Ahern, P Sturmfels, P Venkatesh… - Science, 2024 - science.org
Deep-learning methods have revolutionized protein structure prediction and design but are
presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which …

Cell-free chemoenzymatic starch synthesis from carbon dioxide

T Cai, H Sun, J Qiao, L Zhu, F Zhang, J Zhang, Z Tang… - Science, 2021 - science.org
Starches, a storage form of carbohydrates, are a major source of calories in the human diet
and a primary feedstock for bioindustry. We report a chemical-biochemical hybrid pathway …

Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of Huanglian Jiedu Decoction against sepsis

X Li, S Wei, S Niu, X Ma, H Li, M Jing, Y Zhao - Computers in biology and …, 2022 - Elsevier
Abstract Background Huanglian Jiedu Decoction (HLJDD) is a classical herbal formula with
potential efficacy in the treatment of sepsis. However, the main components and potential …

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 structural biology community assessment of AlphaFold2 applications

M Akdel, DEV Pires, EP Pardo, J Jänes… - Nature Structural & …, 2022 - nature.com
Most proteins fold into 3D structures that determine how they function and orchestrate the
biological processes of the cell. Recent developments in computational methods for protein …

Bayesian reaction optimization as a tool for chemical synthesis

BJ Shields, J Stevens, J Li, M Parasram, F Damani… - Nature, 2021 - nature.com
Reaction optimization is fundamental to synthetic chemistry, from optimizing the yield of
industrial processes to selecting conditions for the preparation of medicinal candidates …

Equivariant 3D-conditional diffusion model for molecular linker design

I Igashov, H Stärk, C Vignac, A Schneuing… - Nature Machine …, 2024 - nature.com
Fragment-based drug discovery has been an effective paradigm in early-stage drug
development. An open challenge in this area is designing linkers between disconnected …