The coming of age of de novo protein design
There are 20200 possible amino-acid sequences for a 200-residue protein, of which the
natural evolutionary process has sampled only an infinitesimal subset. De novo protein …
natural evolutionary process has sampled only an infinitesimal subset. De novo protein …
The importance of catalytic promiscuity for enzyme design and evolution
The ability of one enzyme to catalyse multiple, mechanistically distinct transformations likely
played a crucial role in organisms' abilities to adapt to changing external stimuli in the past …
played a crucial role in organisms' abilities to adapt to changing external stimuli in the past …
Single-sequence protein structure prediction using a language model and deep learning
AlphaFold2 and related computational systems predict protein structure using deep learning
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …
Systems metabolic engineering of microorganisms for natural and non-natural chemicals
Growing concerns over limited fossil resources and associated environmental problems are
motivating the development of sustainable processes for the production of chemicals, fuels …
motivating the development of sustainable processes for the production of chemicals, fuels …
Computational protein design enables a novel one-carbon assimilation pathway
We describe a computationally designed enzyme, formolase (FLS), which catalyzes the
carboligation of three one-carbon formaldehyde molecules into one three-carbon …
carboligation of three one-carbon formaldehyde molecules into one three-carbon …
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
Navigating the landscape of enzyme design: from molecular simulations to machine learning
J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
Computational enzyme design
Recent developments in computational chemistry and biology have come together in the
“inside‐out” approach to enzyme engineering. Proteins have been designed to catalyze …
“inside‐out” approach to enzyme engineering. Proteins have been designed to catalyze …
Computational design of ligand-binding proteins with high affinity and selectivity
The ability to design proteins with high affinity and selectivity for any given small molecule is
a rigorous test of our understanding of the physiochemical principles that govern molecular …
a rigorous test of our understanding of the physiochemical principles that govern molecular …
[HTML][HTML] Directed evolution of a selective and sensitive serotonin sensor via machine learning
Serotonin plays a central role in cognition and is the target of most pharmaceuticals for
psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will …
psychiatric disorders. Existing drugs have limited efficacy; creation of improved versions will …