StarPepWeb: an integrative, graph-based resource for bioactive peptides
Journal
Bioinformatics Advances
ISSN
2635-0041
Publisher
Oxford University Press (OUP)
Date Issued
2024-12-26
Author(s)
Christian López
Roberto Cárdenas
Longendri Aguilera-Mendoza
Guillermin Agüero-Chapin
César R García-Jacas
Noel Pérez-Pérez
Type
text::journal::journal article
Abstract
<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Motivation</jats:title>
<jats:p>The rapid growth of bioactive peptide sequences presents challenges for organization and analysis. Existing repositories often specialize in functions, taxonomic origins, or structural classes, but most remain isolated, use heterogeneous metadata, and lack uniform descriptors or structural models. Few integrative web services exist, offering only partial coverage or depth. As a result, reproducible and comprehensive exploration of the bioactive peptide landscape remains limited, underscoring the need for a unified, source-tracked, extensible platform.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>We present StarPepWeb, a freely accessible web application that democratizes access to StarPepDB, one of the largest curated repositories of bioactive peptides. The platform integrates 45 120 non-redundant sequences from 40 public databases into a source-tracked graph enriched with metadata, physicochemical features, and predicted 3D structures from ESMFold. Each peptide is represented with ESM-2 embeddings and iFeature descriptors, while the interface supports metadata-aware filtering, alignment-based similarity searches with single and multiple queries, and interactive visualization. A microservice-oriented architecture ensures scalability, maintainability, and reproducible versioned downloads, including Neo4j exports. StarPepWeb thus overcomes deployment and expertise barriers of the standalone database, providing an extensible, cloud-hosted framework for integrative bioactive peptide analysis.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>StarPepWeb is freely available at https://starpepweb.org. Source code and documentation are hosted at https://github.com/starpep-web.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Motivation</jats:title>
<jats:p>The rapid growth of bioactive peptide sequences presents challenges for organization and analysis. Existing repositories often specialize in functions, taxonomic origins, or structural classes, but most remain isolated, use heterogeneous metadata, and lack uniform descriptors or structural models. Few integrative web services exist, offering only partial coverage or depth. As a result, reproducible and comprehensive exploration of the bioactive peptide landscape remains limited, underscoring the need for a unified, source-tracked, extensible platform.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>We present StarPepWeb, a freely accessible web application that democratizes access to StarPepDB, one of the largest curated repositories of bioactive peptides. The platform integrates 45 120 non-redundant sequences from 40 public databases into a source-tracked graph enriched with metadata, physicochemical features, and predicted 3D structures from ESMFold. Each peptide is represented with ESM-2 embeddings and iFeature descriptors, while the interface supports metadata-aware filtering, alignment-based similarity searches with single and multiple queries, and interactive visualization. A microservice-oriented architecture ensures scalability, maintainability, and reproducible versioned downloads, including Neo4j exports. StarPepWeb thus overcomes deployment and expertise barriers of the standalone database, providing an extensible, cloud-hosted framework for integrative bioactive peptide analysis.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>StarPepWeb is freely available at https://starpepweb.org. Source code and documentation are hosted at https://github.com/starpep-web.</jats:p>
</jats:sec>