Protein remote homology detection and structural alignment using deep learning
Exploiting sequence–structure–function relationships in biotechnology requires improved
methods for aligning proteins that have low sequence similarity to previously annotated …
methods for aligning proteins that have low sequence similarity to previously annotated …
Valorization of single-carbon chemicals by using carboligases as key enzymes
H Cheon, JH Kim, JS Kim, JB Park - Current Opinion in Biotechnology, 2024 - Elsevier
Highlights•C1 compounds can be converted into formaldehyde.•Formaldehyde can be
condensed into multicarbon products by C1 carboligases.•Enzyme and metabolic …
condensed into multicarbon products by C1 carboligases.•Enzyme and metabolic …
Widespread Distribution of the arsO Gene Confers Bacterial Resistance to Environmental Antimony
ST Tang, XW Song, J Chen, J Shen, B Ma… - Environmental …, 2023 - ACS Publications
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 …
antimony (Sb) detoxification mechanism. Ensifer adhaerens ST2, a bacterial isolate from a …
Sequencing-based analysis of microbiomes
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 …
have varied functional roles that have an impact on agriculture, environmental sciences, and …
Insights into the inner workings of transformer models for protein function prediction
M Wenzel, E Grüner, N Strodthoff - Bioinformatics, 2024 - academic.oup.com
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 …
into the inner workings of neural networks for protein function prediction, by extending the …
Fast protein structure searching using structure graph embeddings
JG Greener, K Jamali - bioRxiv, 2022 - biorxiv.org
Comparing and searching protein structures independent of primary sequence has proved
useful for remote homology detection, function annotation and protein classification. With the …
useful for remote homology detection, function annotation and protein classification. With the …
Learning from the unknown: exploring the range of bacterial functionality
Determining the repertoire of a microbe's molecular functions is a central question in
microbial biology. Modern techniques achieve this goal by comparing microbial genetic …
microbial biology. Modern techniques achieve this goal by comparing microbial genetic …
TM-Vec: template modeling vectors for fast homology detection and alignment
Exploiting sequence-structure-function relationships in molecular biology and computational
modeling relies on detecting proteins with high sequence similarities. However, the most …
modeling relies on detecting proteins with high sequence similarities. However, the most …
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins
Recent advances in Artificial Intelligence and Machine Learning (eg., AlphaFold,
RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures …
RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures …
Navigating the landscape of enzyme design: from molecular simulations to machine learning
J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …