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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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A peptide bond covalently attaches amino acids through a dehydration reaction. One amino acid's carboxyl group and another amino acid's amino group combine, releasing a water molecule. The resulting bond is the peptide bond. The products that such linkages form are peptides. As more amino acids join this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end has the N-terminal, or the amino-terminal, and the other end has a free...
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Identifying Protein-protein Interaction Sites Using Peptide Arrays
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StarPepWeb: an integrative, graph-based resource for bioactive peptides.

Christian López1, Roberto Cárdenas1, Longendri Aguilera-Mendoza2

  • 1Colegio de Ciencias e Ingenierías "El Politécnico", Universidad San Francisco de Quito USFQ, Quito 170157, Ecuador.

Bioinformatics Advances
|December 15, 2025
PubMed
Summary
This summary is machine-generated.

StarPepWeb offers a unified platform for analyzing bioactive peptides, integrating diverse data into a searchable graph. This web application democratizes access to curated peptide sequences, enabling comprehensive exploration and analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Peptide Science

Background:

  • Bioactive peptide sequences are rapidly growing, posing challenges for organization and analysis.
  • Existing peptide repositories are often isolated, use heterogeneous metadata, and lack uniform descriptors.
  • Limited integrative web services hinder reproducible and comprehensive exploration of bioactive peptides.

Purpose of the Study:

  • To present StarPepWeb, a freely accessible web application for democratizing access to StarPepDB, a large curated bioactive peptide repository.
  • To provide a unified, source-tracked, and extensible platform for integrative bioactive peptide analysis.
  • To overcome barriers to accessing and analyzing bioactive peptide data.

Main Methods:

  • Integrated 45,120 non-redundant bioactive peptide sequences from 40 public databases into a source-tracked graph.
  • Enriched the graph with metadata, physicochemical features, and predicted 3D structures (ESMFold).
  • Utilized ESM-2 embeddings and iFeature descriptors for each peptide, implementing metadata-aware filtering and alignment-based similarity searches.

Main Results:

  • Developed StarPepWeb, a web application offering metadata-aware filtering, similarity searches, and interactive visualization.
  • Implemented a microservice-oriented architecture for scalability, maintainability, and reproducible versioned downloads (including Neo4j exports).
  • Provided a cloud-hosted framework overcoming deployment and expertise barriers for standalone databases.

Conclusions:

  • StarPepWeb provides a unified, extensible, and user-friendly framework for the integrative analysis of bioactive peptides.
  • The platform democratizes access to a vast curated peptide repository, facilitating research and discovery.
  • StarPepWeb addresses the need for a comprehensive and reproducible approach to bioactive peptide exploration.