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 …
A user's guide to cell-free protein synthesis
Cell-free protein synthesis (CFPS) is a platform technology that provides new opportunities
for protein expression, metabolic engineering, therapeutic development, education, and …
for protein expression, metabolic engineering, therapeutic development, education, and …
Generative models for graph-based protein design
Engineered proteins offer the potential to solve many problems in biomedicine, energy, and
materials science, but creating designs that succeed is difficult in practice. A significant …
materials science, but creating designs that succeed is difficult in practice. A significant …
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 …
De novo gene birth
SB Van Oss, AR Carvunis - PLoS genetics, 2019 - journals.plos.org
De novo gene birth is the process by which new genes evolve from DNA sequences that
were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be …
were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be …
[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …
molecules. Thus, one may obtain biological insights into protein functions, disease …
Catalytic DNA: scope, applications, and biochemistry of deoxyribozymes
SK Silverman - Trends in biochemical sciences, 2016 - cell.com
The discovery of natural RNA enzymes (ribozymes) prompted the pursuit of artificial DNA
enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual …
enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual …
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 …
Exploring protein fitness landscapes by directed evolution
Directed evolution circumvents our profound ignorance of how a protein's sequence
encodes its function by using iterative rounds of random mutation and artificial selection to …
encodes its function by using iterative rounds of random mutation and artificial selection to …
Root of the tree: the significance, evolution, and origins of the ribosome
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life.
Made from RNA and protein, the ribosome translates mRNA to coded protein in all living …
Made from RNA and protein, the ribosome translates mRNA to coded protein in all living …