AIMC Topic: Molecular Sequence Annotation
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Improving viral annotation with artificial intelligence.
mBio
Sep 4, 2024
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environme...
Multi-modal deep learning enables efficient and accurate annotation of enzymatic active sites.
Nature communications
Aug 27, 2024
Annotating active sites in enzymes is crucial for advancing multiple fields including drug discovery, disease research, enzyme engineering, and synthetic biology. Despite the development of numerous automated annotation algorithms, a significant trad...
Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models.
Microbial pathogenesis
Jun 6, 2024
Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat t...
Vocabulary Matters: An Annotation Pipeline and Four Deep Learning Algorithms for Enzyme Named Entity Recognition.
Journal of proteome research
May 11, 2024
Enzymes are indispensable in many biological processes, and with biomedical literature growing exponentially, effective literature review becomes increasingly challenging. Natural language processing methods offer solutions to streamline this process...
KEGG orthology prediction of bacterial proteins using natural language processing.
BMC bioinformatics
Apr 11, 2024
BACKGROUND: The advent of high-throughput technologies has led to an exponential increase in uncharacterized bacterial protein sequences, surpassing the capacity of manual curation. A large number of bacterial protein sequences remain unannotated by ...
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding.
Genome biology
Feb 1, 2024
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational methods have been developed. However, the existing methods suffer from a serious long-tail problem, with a large number of GO famili...
Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
Nature communications
Nov 14, 2023
Functional annotation of open reading frames in microbial genomes remains substantially incomplete. Enzymes constitute the most prevalent functional gene class in microbial genomes and can be described by their specific catalytic functions using the ...
Uncovering new families and folds in the natural protein universe.
Nature
Sep 13, 2023
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database. These models cover nearly all proteins that are known, including thos...
Enzyme function prediction using contrastive learning.
Science (New York, N.Y.)
Mar 30, 2023
Enzyme function annotation is a fundamental challenge, and numerous computational tools have been developed. However, most of these tools cannot accurately predict functional annotations, such as enzyme commission (EC) number, for less-studied protei...
Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.
mSystems
Mar 7, 2023
Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new m...
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