MassSpecBlocks

MassSpecBlocks converts chemical structures in SMILES into building-block sequences and enables creation of custom sequence and building-block databases for annotation of nonribosomal peptides (NRPs) and polyketides.

Key Features:

• Structure conversion and sequence generation: Converts SMILES input into sequences of building blocks, handling uncommon amino acids and cyclic, branched, and branch-cyclic architectures.
• Database integration and editing: Integrates with PubChem, ChemSpider, ChEBI, NP Atlas, COCONUT, and Norine for searching, retrieval, and editing of chemical structures.
• Custom database creation: Constructs custom sequence and building-block databases for annotating mass spectra, including support for polyketide siderophores and diverse NRP topologies.
• Export functionality: Exports sequences and building blocks into plain-text formats compatible with CycloBranch for spectral annotation.
• Programmatic interoperability: Provides a REST API for integration with other bioinformatics tools and workflows.

Scientific Applications:

• NRP and polyketide structural characterization: Supports interpretation of high-resolution tandem mass spectrometry data by supplying building-block sequences and tailored databases.
• Spectral annotation: Enables annotation of linear, cyclic, branched, and branch-cyclic NRPs and polyketide siderophores through CycloBranch-compatible exports and custom databases.

Methodology:

Accepts SMILES-format structures, integrates searches and edits with PubChem, ChemSpider, ChEBI, NP Atlas, COCONUT, and Norine, supports creation of custom sequence and building-block databases, and exports plain-text files compatible with CycloBranch, with programmatic access via a REST API.