Microbiomes occupy a range of niches and, in addition to having diverse compositions, they
have varied functional roles that have an impact on agriculture, environmental sciences, and …

Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …

Exploiting sequence–structure–function relationships in biotechnology requires improved
methods for aligning proteins that have low sequence similarity to previously annotated …

Protein language models (pLMs) capture some aspects of the grammar of the language of
life as written in protein sequences. The so-called pLM embeddings implicitly contain this …

Microbial oxidation of environmental antimonite (Sb (III)) to antimonate (Sb (V)) is an
antimony (Sb) detoxification mechanism. Ensifer adhaerens ST2, a bacterial isolate from a …

Archaea are vital components of the human microbiome, yet their study within the
gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study …

Motivation We explored how explainable artificial intelligence (XAI) can help to shed light
into the inner workings of neural networks for protein function prediction, by extending the …

Background The extreme environment of the International Space Station (ISS) puts selective
pressure on microorganisms unintentionally introduced during its 20+ years of service as a …

Recent advances in Artificial Intelligence and Machine Learning (eg., AlphaFold,
RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures …

Protein engineering is a pivotal aspect of synthetic biology, involving the modification of
amino acids within existing protein sequences to achieve novel or enhanced functionalities …