AIMC Topic: Databases, Protein

Clear Filters Showing 1 to 10 of 713 articles

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...
Proteome Glycosylation Mice, Inbred C57BL Mice Proteomics Neurodegenerative Diseases Alzheimer Disease Glycopeptides Humans Parkinson Disease Glycoproteins Brain Databases, Protein Animals Male Aging
View on PubMed DOI

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...
Databases, Protein Deep Learning Protein Conformation Algorithms Computational Biology Models, Molecular Protein Domains Proteins
View on PubMed DOI

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 Algorithms Computational Biology Humans Machine Learning
View on PubMed DOI

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 Humans Neural Networks, Computer Algorithms Deep Learning Computational Biology
View on PubMed DOI

A new strategy for Cas protein recognition based on graph neural networks and SMILES encoding.

Scientific reports Apr 30, 2025
The CRISPR-Cas system, an adaptive immune mechanism found in bacteria and archaea, has evolved into a promising genomic editing tool, with various types of Cas proteins playing a crucial role. In this study, we developed a set of strategies for minin...
CRISPR-Cas Systems Neural Networks, Computer CRISPR-Associated Proteins Graph Neural Networks Computational Biology Databases, Protein
View on PubMed DOI

Deep Learning-Based Prediction of Decoy Spectra for False Discovery Rate Estimation in Spectral Library Searching.

Journal of proteome research Apr 19, 2025
With the advantage of extensive coverage, predicted spectral libraries are becoming an attractive alternative in proteomic data analysis. As a popular false discovery rate estimation method, target decoy search has been adopted in library search work...
Proteomics Databases, Protein Tandem Mass Spectrometry Deep Learning Peptide Library
View on PubMed DOI

ESM-Ezy: a deep learning strategy for the mining of novel multicopper oxidases with superior properties.

Nature communications Apr 6, 2025
The UniProt database is a valuable resource for biocatalyst discovery, yet predicting enzymatic functions remains challenging, especially for low-similarity sequences. Identifying superior enzymes with enhanced catalytic properties is even harder. To...
Deep Learning Databases, Protein Hydrogen-Ion Concentration Data Mining Biocatalysis Oxidoreductases
View on PubMed DOI

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...
Deep Learning Protein Binding Computational Biology Humans Neural Networks, Computer Algorithms Sequence Analysis, Protein Amino Acid Sequence Protein Conformation Protein Interaction Mapping Proteins Databases, Protein
View on PubMed DOI

Learning the rules of peptide self-assembly through data mining with large language models.

Science advances Mar 26, 2025
Peptides are ubiquitous and important biomolecules that self-assemble into diverse structures. Although extensive research has explored the effects of chemical composition and exterior conditions on self-assembly, a systematic study consolidating the...
Algorithms Humans Peptides Machine Learning Data Mining Databases, Protein
View on PubMed DOI

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...
Databases, Protein Binding Sites Sequence Analysis, Protein Computational Biology Proteins Neural Networks, Computer Algorithms Deep Learning Protein Binding
View on PubMed DOI
Popular Topics
Recent Journals