Machine learning of reaction properties via learned representations of the condensed graph of reaction
The estimation of chemical reaction properties such as activation energies, rates, or yields is
a central topic of computational chemistry. In contrast to molecular properties, where …
a central topic of computational chemistry. In contrast to molecular properties, where …
Genomic enzymology: web tools for leveraging protein family sequence–function space and genome context to discover novel functions
JA Gerlt - Biochemistry, 2017 - ACS Publications
The exponentially increasing number of protein and nucleic acid sequences provides
opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural …
opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural …
Contrastive learning in protein language space predicts interactions between drugs and protein targets
Sequence-based prediction of drug–target interactions has the potential to accelerate drug
discovery by complementing experimental screens. Such computational prediction needs to …
discovery by complementing experimental screens. Such computational prediction needs to …
Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis
A systems-level understanding of Gram-positive bacteria is important from both an
environmental and health perspective and is most easily obtained when high-quality …
environmental and health perspective and is most easily obtained when high-quality …
Expanding functional protein sequence spaces using generative adversarial networks
D Repecka, V Jauniskis, L Karpus… - Nature Machine …, 2021 - nature.com
De novo protein design for catalysis of any desired chemical reaction is a long-standing goal
in protein engineering because of the broad spectrum of technological, scientific and …
in protein engineering because of the broad spectrum of technological, scientific and …
Machine learning modeling of family wide enzyme-substrate specificity screens
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex
natural products, and commodity chemicals at scale. However, the adoption of biocatalysis …
natural products, and commodity chemicals at scale. However, the adoption of biocatalysis …
Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics
Unculturable bacterial communities provide a rich source of biocatalysts, but their
experimental discovery by functional metagenomics is difficult, because the odds are …
experimental discovery by functional metagenomics is difficult, because the odds are …
De novo artificial synthesis of hexoses from carbon dioxide
J Yang, W Song, T Cai, Y Wang, X Zhang, W Wang… - Science Bulletin, 2023 - Elsevier
Abstract Developing artificial “CO 2-sugar” platforms is meaningful for addressing
challenges posed by land scarcity and climate change to the supply of dietary sugar …
challenges posed by land scarcity and climate change to the supply of dietary sugar …
Shining a light on enzyme promiscuity
SD Copley - Current opinion in structural biology, 2017 - Elsevier
Highlights•Screening efforts have revealed enzymes with over 100 promiscuous
activities.•High-throughput screening for promiscuous activities can be accomplished in …
activities.•High-throughput screening for promiscuous activities can be accomplished in …
Gene3D: extensive prediction of globular domains in proteins
Abstract Gene3D (http://gene3d. biochem. ucl. ac. uk) is a database of globular domain
annotations for millions of available protein sequences. Gene3D has previously featured in …
annotations for millions of available protein sequences. Gene3D has previously featured in …