View the User Guide at Grupo-Medicina-Molecular-y-Traslacional.github.io/StarPep_doc.
StarPep toolbox is a software for studying the antimicrobial peptides' (AMPs) chemical space with molecular network-based representations and similarity searching models. This application aims to contribute to peptide drug repurposing, development, and optimization.
This tool was developed as a Java desktop application that integrates the functionalities of several open-source projects. The graphical user interface was built on top of the NetBeans Platform, using the Java SE Runtime Environment 8. The graph database structure was implemented with the Neo4j platform. Some visualization features and the calculation of network properties were based on Gephi. The sequence alignment algorithms were implemented using the BioJava API.
The AMPs were collected from a large variety of biological data sources to be organized into an integrated graph database called starPepDB, composed of 45.120 AMPs and their metadata. This integrated graph database is embedded in StarPep toolbox to enable end-user querying, filtering, visualizing, and analyzing the AMPs taking advantage of network-based representations.
The main features of StarPep toolbox are listed below:
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AMPs' chemical space filtering: obtain a subset of AMPs from the StarPepDB using their metadata (function, target pathogen, biological origin, chemical modifications, original database, and cross-referenced entries to PDB, PubMed, and UniProt).
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Molecular descriptors: calculate molecular descriptors of the AMPs by applying statistical and aggregation operators on physicochemical amino acid properties (e.g., net charge, isoelectric point, molecular weight, etc.).
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Network Science: build different types of networks (metadata, chemical space, and half-space proximal) and calculate global/local properties, centrality metrics, communities, etc.
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Similarity searching: create multi-query similarity searching models that can lead to the repurposing of AMPs with novel functional activities.
You can find the source code of StarPep in this GitHub repository.
Special thanks to the developers of quarto. We deployed this site with the quarto publish command and GitHub action alternative. An example of how to use this method is available in this Github repository.