11. Limitations and alternatives

BpForms has a few known limitations. Here we describe these limitations and, where possible suggest alternative solutions.

• BpForms cannot represent the secondary structure (e.g., base pairing) of biopolymers. Extending BpForms to represent secondary structure would enable BpForms to represent more DNA forms involved in DNA damage and repair.
• BpForms cannot represent branched biopolymers such as carbohydrates. Other formats such as WURCS are better suited for this purpose. See Glycopedia for more information.
• BpForms cannot represent the three-dimensional structure of a polymer. The PDB format is better suited for this purpose.