AIMC Topic: Sequence Analysis, Protein

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Bag-of-words is competitive with sum-of-embeddings language-inspired representations on protein inference.

PloS one Aug 6, 2025
Inferring protein function is a fundamental and long-standing problem in biology. Laboratory experiments in this field are often expensive, and therefore large-scale computational protein inference from readily available amino acid sequences is neede...
Algorithms Computational Biology Natural Language Processing Amino Acid Sequence Sequence Analysis, Protein Proteins Databases, Protein
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Rprot-Vec: a deep learning approach for fast protein structure similarity calculation.

BMC bioinformatics Jul 10, 2025
BACKGROUND: Predicting protein structural similarity and detecting homologous sequences remain fundamental and challenging tasks in computational biology. Accurate identification of structural homologs enables function inference for newly discovered ...
Sequence Analysis, Protein Databases, Protein Protein Conformation Deep Learning Computational Biology Proteins Software
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A fast (CNN + MCWS-transformer) based architecture for protein function prediction.

Statistical applications in genetics and molecular biology Jul 1, 2025
The transformer model for sequence mining has brought a paradigmatic shift to many domains, including biological sequence mining. However, transformers suffer from quadratic complexity, i.e., O( ), where is the sequence length, which affects the tra...
Sequence Analysis, Protein Proteins Databases, Protein Algorithms Computational Biology Neural Networks, Computer
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The AI revolution comes to protein sequencing.

Science (New York, N.Y.) Apr 10, 2025
By identifying unknown proteins, new systems could aid research in many areas.
Artificial Intelligence Humans Proteins Sequence Analysis, Protein
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TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning.

Communications biology Apr 5, 2025
Identifying DNA-binding proteins and their binding residues is critical for understanding diverse biological processes, but conventional experimental approaches are slow and costly. Existing machine learning methods, while faster, often lack accuracy...
DNA-Binding Proteins Sequence Alignment Sequence Analysis, Protein Deep Learning Computational Biology Humans Software
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SeqNovo: De Novo Peptide Sequencing Prediction in IoMT via Seq2Seq.

IEEE journal of biomedical and health informatics Apr 4, 2025
In the Internet of Medical Things (IoMT), de novo peptide sequencing prediction is one of the most important techniques for the fields of disease prediction, diagnosis, and treatment. Recently, deep-learning-based peptide sequencing prediction has be...
Humans Algorithms Computational Biology Peptides Deep Learning Sequence Analysis, Protein
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Predicting protein-protein interaction with interpretable bilinear attention network.

Computer methods and programs in biomedicine Mar 30, 2025
BACKGROUND AND OBJECTIVE: Protein-protein interactions (PPIs) play the key roles in myriad biological processes, helping to understand the protein function and disease pathology. Identification of PPIs and their interaction types through wet experime...
Protein Interaction Mapping Sequence Analysis, Protein Amino Acid Sequence Protein Conformation Proteins Databases, Protein Neural Networks, Computer Algorithms Protein Binding Computational Biology Deep Learning Humans
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Deep-ProBind: binding protein prediction with transformer-based deep learning model.

BMC bioinformatics Mar 22, 2025
Binding proteins play a crucial role in biological systems by selectively interacting with specific molecules, such as DNA, RNA, or peptides, to regulate various cellular processes. Their ability to recognize and bind target molecules with high speci...
Computational Biology Proteins Binding Sites Sequence Analysis, Protein Deep Learning Neural Networks, Computer Databases, Protein Protein Binding Algorithms
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GRATCR: Epitope-Specific T Cell Receptor Sequence Generation With Data-Efficient Pre-Trained Models.

IEEE journal of biomedical and health informatics Mar 6, 2025
T cell receptors (TCRs) play a crucial role in numerous immunotherapies targeting tumor cells. However, their acquisition and optimization present significant challenges, involving laborious and time-consuming wet lab experimental resource. Deep gene...
Deep Learning Receptors, Antigen, T-Cell Computational Biology Humans Epitopes, T-Lymphocyte Sequence Analysis, Protein
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Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Algorithms Deep Learning Proteins Databases, Protein Models, Molecular Computational Biology Cluster Analysis Protein Conformation Sequence Analysis, Protein Protein Domains Sequence Alignment Amino Acid Sequence
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