Počet záznamů: 1  

MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis

  1. 1.
    0543988 - MBÚ 2022 RIV GB eng J - Článek v odborném periodiku
    Přívratský, J. - Novák, Jiří
    MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.
    Journal of Cheminformatics. Roč. 13, č. 1 (2021), č. článku 51. ISSN 1758-2946. E-ISSN 1758-2946
    Grant CEP: GA ČR(CZ) GA21-17044S
    Institucionální podpora: RVO:61388971
    Klíčová slova: Mass spectrometry * Building blocks * Nonribosomal petides * Polyketides * Siderophores * MassSpecBlocks * CycloBranch * Tanimoto similarity * SmilesDrawer
    Obor OECD: Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
    Impakt faktor: 8.489, rok: 2021
    Způsob publikování: Open access
    https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00530-2

    Nonribosomal peptides and polyketides are natural products commonly synthesized by microorganisms. They are widely used in medicine, agriculture, environmental protection, and other fields. The structures of natural products are often analyzed by high-resolution tandem mass spectrometry, which becomes more popular with its increasing availability. However, the characterization of nonribosomal peptides and polyketides from tandem mass spectra is a nontrivial task because they are composed of many uncommon building blocks in addition to proteinogenic amino acids. Moreover, many of them have cyclic and branch-cyclic structures. Here, we introduce MassSpecBlocks an opensource and web-based tool that converts the input chemical structures in SMILES format into sequences of building blocks. The structures can be searched in public databases PubChem, ChemSpider, ChEBI, NP Atlas, COCONUT, and Norine and edited in a user-friendly graphical interface. Although MassSpecBlocks can serve as a stand-alone database, our primary goal was to enable easy construction of custom sequence and building block databases, which can be used to annotate mass spectra in CycloBranch software. CycloBranch is an open-source, cross-platform, and standalone tool that we recently released for annotating spectra of linear, cyclic, branched, and branch-cyclic nonribosomal peptides and polyketide siderophores. The sequences and building blocks created in MassSpecBlocks can be easily exported into a plain text format used by CycloBranch. MassSpecBlocks is available online or can be installed entirely offline. It offers a REST API to cooperate with other tools.
    Trvalý link: http://hdl.handle.net/11104/0321068

     
     
Počet záznamů: 1  

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