In the traditional SCSR representation each RNA/DNA sequence atom represented a full nucleotide:
With the introduction of the HELM format, RNA/DNA sequences could now be represented with their sugar, base and phosphate building blocks individually:
With the BIOVIA 2020 release the granular MOL format extension was introduced. Nucleotides can now be split into separate sugar/base/phosphate entities which accommodates the use of modified entities of these types. It also allows more control over the position of the terminal phosphate groups (at the 3’ or 5’ end of the sequence). The granular representation also results in more consistent inter-conversion with the HELM format.
BIOVIA Draw will continue to support both formats, the granular as well as the full nucleotide representation. Sketching sequences in granular format is enabled via right-clicking on the sequence atoms. Sugars/bases/phosphates can be selected individually. The resulting sequence will still be displayed as compact sequence string. Any change of sugar/base/phosphate is treated as modification (colored red). A change of the base template causes the nucleotide sequence atom to be renamed.
Granular and full nucleotide representation are equivalent. In BIOVIA Draw a granular MOL file can be created in two ways:
- „Copy as“-> „granular molfile“
- „Export Sequence“ -> „granular format“
Opening the granular MOl file in Pipette BioSketcher (File -> Launch Editor -> Pipette Sketcher) displays it in HELM depiction:
