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 …
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 …
<? sty\usepackage {wasysym}?> Bilingual language model for protein sequence and structure
Adapting language models to protein sequences spawned the development of powerful
protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein …
protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein …
AbDiffuser: full-atom generation of in-vitro functioning antibodies
We introduce AbDiffuser, an equivariant and physics-informed diffusion model for the joint
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
generation of antibody 3D structures and sequences. AbDiffuser is built on top of a new …
Protein generation with evolutionary diffusion: sequence is all you need
Deep generative models are increasingly powerful tools for the in silico design of novel
proteins. Recently, a family of generative models called diffusion models has demonstrated …
proteins. Recently, a family of generative models called diffusion models has demonstrated …
Accurate prediction of protein function using statistics-informed graph networks
Understanding protein function is pivotal in comprehending the intricate mechanisms that
underlie many crucial biological activities, with far-reaching implications in the fields of …
underlie many crucial biological activities, with far-reaching implications in the fields of …
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
We seek to transform how new and emergent variants of pandemic-causing viruses,
specifically SARS-CoV-2, are identified and classified. By adapting large language models …
specifically SARS-CoV-2, are identified and classified. By adapting large language models …
Computational scoring and experimental evaluation of enzymes generated by neural networks
In recent years, generative protein sequence models have been developed to sample novel
sequences. However, predicting whether generated proteins will fold and function remains …
sequences. However, predicting whether generated proteins will fold and function remains …
Accelerating biocatalysis discovery with machine learning: a paradigm shift in enzyme engineering, discovery, and design
B Markus, K Andreas, K Arkadij, L Stefan, O Gustav… - ACS …, 2023 - ACS Publications
Emerging computational tools promise to revolutionize protein engineering for biocatalytic
applications and accelerate the development timelines previously needed to optimize an …
applications and accelerate the development timelines previously needed to optimize an …
[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 …