BpForms documentation

BpForms is a set of tools for concretely representing the primary structures of non-canonical forms of biopolymers, such as oxidized DNA, methylated RNA, and acetylated proteins, and calculating properties of non-canonical biopolymers.

BpForms emcompasses five tools:

  • A notation for concretely describing the primary structures of non-canonical biopolymers. See Section 2.1 for detailed information. For example, the following represents a modified DNA molecule that contains a deoxyinosine monomeric form at the fourth position:

    ACG[
        id: "dI" | structure: "O=C1NC=NC2=C1N=CN2"
        ]T
    

    This concrete representation enables the BpForms software tools to calculate properties of non-canonical biopolymers.

  • Tools for calculating properties of non-canonical biopolymers including their chemical formulae, molecular weights, charges, and major protonation and tautomerization states.

BpForms was motivated by the need to concretely represent the biochemistry of DNA modification, DNA repair, post-transcriptional processing, and post-translational processing in whole-cell computational models. BpForms is also a valuable tool for experimental proteomics and synthetic biology. In particular, we developed BpForms because there were no notations, schemas, data models, or file formats for concretely representing modified forms of biopolymers, despite the existence of several databases and ontologies of DNA, RNA, and protein modifications, the ProForma Proteoform Notation, and the MOMODICS codes for modified RNA bases.

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