Machine learning-guided protein engineering
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …
machine learning methods. These methods leverage existing experimental and simulation …
Machine learning for functional protein design
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and
structure data have radically transformed computational protein design. New methods …
structure data have radically transformed computational protein design. New methods …
Proteingym: Large-scale benchmarks for protein fitness prediction and design
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …
understanding genetic disease to designing novel proteins to address our most pressing …
Rapid protein stability prediction using deep learning representations
Predicting the thermodynamic stability of proteins is a common and widely used step in
protein engineering, and when elucidating the molecular mechanisms behind evolution and …
protein engineering, and when elucidating the molecular mechanisms behind evolution and …
Opportunities and challenges for machine learning-assisted enzyme engineering
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
Transfer learning to leverage larger datasets for improved prediction of protein stability changes
H Dieckhaus, M Brocidiacono… - Proceedings of the …, 2024 - National Acad Sciences
Amino acid mutations that lower a protein's thermodynamic stability are implicated in
numerous diseases, and engineered proteins with enhanced stability can be important in …
numerous diseases, and engineered proteins with enhanced stability can be important in …
Opportunities and challenges in design and optimization of protein function
The field of protein design has made remarkable progress over the past decade. Historically,
the low reliability of purely structure-based design methods limited their application, but …
the low reliability of purely structure-based design methods limited their application, but …
Discovering functionally important sites in proteins
Proteins play important roles in biology, biotechnology and pharmacology, and missense
variants are a common cause of disease. Discovering functionally important sites in proteins …
variants are a common cause of disease. Discovering functionally important sites in proteins …
[HTML][HTML] De novo protein design—From new structures to programmable functions
T Kortemme - Cell, 2024 - cell.com
Methods from artificial intelligence (AI) trained on large datasets of sequences and
structures can now" write" proteins with new shapes and molecular functions de novo …
structures can now" write" proteins with new shapes and molecular functions de novo …
A combinatorially complete epistatic fitness landscape in an enzyme active site
Protein engineering often targets binding pockets or active sites which are enriched in
epistasis—nonadditive interactions between amino acid substitutions—and where the …
epistasis—nonadditive interactions between amino acid substitutions—and where the …