AIMC Topic: Databases, Protein

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MESM: integrating multi-source data for high-accuracy protein-protein interactions prediction through multimodal language models.

BMC biology Aug 11, 2025
BACKGROUND: Protein-protein interactions (PPIs) play a critical role in essential biological processes such as signal transduction, enzyme activity regulation, cytoskeletal structure, immune responses, and gene regulation. However, current methods ma...
Humans Neural Networks, Computer Databases, Protein Saccharomyces cerevisiae Protein Interaction Mapping Deep Learning Protein Interaction Maps
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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...
Sequence Analysis, Protein Natural Language Processing Amino Acid Sequence Algorithms Proteins Databases, Protein Computational Biology
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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 ...
Software Sequence Analysis, Protein Proteins Databases, Protein Protein Conformation Deep Learning Computational Biology
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Comprehensive protein datasets and benchmarking for liquid-liquid phase separation studies.

Genome biology Jul 8, 2025
BACKGROUND: Proteins self-organize in dynamic cellular environments by assembling into reversible biomolecular condensates through liquid-liquid phase separation (LLPS). These condensates can comprise single or multiple proteins, with different roles...
Phase Separation Benchmarking Biomolecular Condensates Proteins Databases, Protein Algorithms
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Advancing the accuracy of clathrin protein prediction through multi-source protein language models.

Scientific reports Jul 8, 2025
Clathrin is a key cytoplasmic protein that serves as the predominant structural element in the formation of coated vesicles. Specifically, clarithin enables the scission of newly formed vesicles from the plasma membrane's cytoplasmic face. Efficient ...
Humans Neural Networks, Computer Databases, Protein Clathrin Algorithms Computational Biology
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Ultradeep N-glycoproteome atlas of mouse reveals spatiotemporal signatures of brain aging and neurodegenerative diseases.

Nature communications Jul 1, 2025
The current depth of site-specific N-glycoproteomics is insufficient to fully characterize glycosylation events in biological samples. Herein, we achieve an ultradeep and precision analysis of the N-glycoproteome of mouse tissues by integrating multi...
Alzheimer Disease Glycopeptides Glycoproteins Databases, Protein Neurodegenerative Diseases Mice, Inbred C57BL Parkinson Disease Aging Mice Proteome Glycosylation Proteomics Brain Animals Humans Male
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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...
Neural Networks, Computer Algorithms Proteins Databases, Protein Computational Biology Sequence Analysis, Protein
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M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

BMC bioinformatics May 5, 2025
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...
Models, Molecular Protein Conformation Algorithms Proteins Computational Biology Deep Learning Databases, Protein Protein Domains
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Accurate identification and mechanistic evaluation of pathogenic missense variants with .

Proceedings of the National Academy of Sciences of the United States of America May 2, 2025
Understanding the effects of missense mutations or single amino acid variants (SAVs) on protein function is crucial for elucidating the molecular basis of diseases/disorders and designing rational therapies. We introduce here , a machine learning too...
Proteins Databases, Protein Mutation, Missense Humans Algorithms Machine Learning Computational Biology
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ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.

IEEE transactions on neural networks and learning systems May 2, 2025
Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific fu...
Molecular Sequence Annotation Gene Ontology Sequence Alignment Proteins Databases, Protein Algorithms Deep Learning Computational Biology Humans Neural Networks, Computer
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