AIMC Topic: Molecular Sequence Annotation

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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...
Proteome Klebsiella Infections Klebsiella pneumoniae Computational Biology Molecular Sequence Annotation Genome, Bacterial Sequence Alignment Bacterial Proteins Virulence Factors Humans Machine Learning
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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...
Data Mining Molecular Sequence Annotation Enzymes Deep Learning Humans Natural Language Processing Algorithms
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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 ...
Amino Acid Sequence Molecular Sequence Annotation Genome Natural Language Processing Bacterial Proteins
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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...
Proteins Molecular Sequence Annotation Deep Learning Computational Biology Humans Software
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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 ...
Genome Escherichia coli K12 Open Reading Frames Proteins Molecular Sequence Annotation Deep Learning Escherichia coli
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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...
Internet Amino Acid Sequence Protein Folding Structural Homology, Protein Molecular Sequence Annotation Deep Learning Proteins Databases, Protein
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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...
Computational Biology Proteins Molecular Sequence Annotation Reproducibility of Results Machine Learning Biocatalysis Sequence Analysis, Protein Genomics Enzymes Algorithms
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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...
Humans Molecular Sequence Annotation Deep Learning Metagenome Microbiota Genome, Microbial
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ISPRED-SEQ: Deep Neural Networks and Embeddings for Predicting Interaction Sites in Protein Sequences.

Journal of molecular biology Jan 13, 2023
The knowledge of protein-protein interaction sites (PPIs) is crucial for protein functional annotation. Here we address the problem focusing on the prediction of putative PPIs considering as input protein sequences. The issue is important given the h...
Protein Interaction Mapping Amino Acid Sequence Molecular Sequence Annotation Deep Learning Proteins
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DeepPlnc: Bi-modal deep learning for highly accurate plant lncRNA discovery.

Genomics Aug 2, 2022
We present here a bi-modal CNN based deep-learning system, DeepPlnc, to identify plant lncRNAs with high accuracy while using sequence and structural properties. Unlike most of the existing software, it works accurately even in conditions with ambigu...
Plants Molecular Sequence Annotation Software Deep Learning Transcriptome RNA, Long Noncoding
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