Design of metalloproteins and novel protein folds using variational autoencoders
Scientific Reports, 2018. [All Versions]. The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…
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A high-level programming language for generative protein design biorxiv.org
2022. [All Versions]. Combining a basic set of building blocks into more complex forms is a universal design principle. Most protein designs have proceeded from a manual bottom-up approach using parts created by nature, but top-down design of proteins is fundamentally hard due…
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Nature Communications, 2023. [All Versions]. [Project]. Advances in machine learning (ML) and automated experimentation are poised to vastly accelerate research in polymer science. Data representation is a critical aspect for enabling ML integration in research workflows, yet…
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Highly accurate protein structure prediction with AlphaFold nature.com
Nature, 2021. [All Versions]. This paper provides the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. This approach is a canonical application of observation- and explanation…
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Evolution-inspired engineering of nonribosomal peptide synthetases science.org
Science, 2024. [All Versions]. Many clinically used drugs are derived from natural microbial products that are assembled in a stepwise fashion by the condensation of amino acids or acyl groups. Using insights from evolutionary analysis, two independent groups now show that the…
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Protein LM github.com
Implements BERT and autoregressive models for proteins, as described in Biological Structure and Function Emerge from Scaling Unsupervised Learning to 250 Million Protein Sequences and ProGen: Language Modeling for Protein Generation.
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Automated Biodesign Engineering by Abductive Meta-Interpretive Learning arxiv.org
AAAI Spring Symposium Series 2021 on Artificial Intelligence for Synthetic Biology, 2021. [All Versions]. This work proposes an automated biodesign engineering framework empowered by Abductive Meta-Interpretive Learning (MetaAbd), a novel machine learning approach that combines…
AGI & CoCoSci › Papers > Science Logology > AI Assisted Research: “Scientific Reports, 2018. [All Versions]. The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…”