T68-2017: Incorrect conversion from HELM to SCSR and from SCSR to HELM

Collections

An issue has been identified when RNA or DNA biologics represented in HELM format have been converted to the BIOVIA sequence representation SCSR (self-contained sequence representation) (PCHE-7127). The conversion issue is not apparent to the user as the resulting RNA or DNA sequence is shown in the contracted form and inadvertently hides any conversion issues. This affects Pipeline Pilot Chemistry Collection 2017 R2 and products relying on the same version:

• BIOVIA Draw 2017 R2
• BIOVIA Direct 2017 R2
• Insight 2017 R2
• Insight for Excel 2017 R2
• Biological Registration 2017 R2
• Chemical Registration 2017 R2
• DiscoveryStudio 2017 R2
• ScienceCloud 2017 R2
• Notebook 2017 R2.

  
Affected workflows:

• Accessing the HELM editor from BIOVIA Draw and creating a sequence and sending this back to Draw.
• Importing a HELM string into BIOVIA Draw.
• Using the HELM editor with BIOVIA Notebook or BIOVIA Biological or Chemical Registration and entering a HELM string either by:
  • pasting into a structure field
  • opening the HELM editor from a structure field and creating a sequence using the HELM editor, then sending the HELM back to the application (where it is automatically converted to SCSR format)
• Using the Pipeline Pilot Chemistry Collection to process sequences generated by any of the following means
  • the HELM editor
  • converting HELM using one of the HELM to Molecule conversion components
  • pasting into the Chemistry Sketcher box (which automatically converts to SCSR format)
• Sending HELM strings to BIOVIA Direct and allowing the Direct cartridge to convert them to the SCSR format
• Opening a HELM file directly from a Chemistry or SCSR field in BIOVIA Biological or Chemical Registration

 
Under very specific circumstance, described below, incorrect structures may have been generated.
 
This issue only occurs with oligonucleotides (RNA/DNA). Conversion is correct when the nucleotides are phosphorylated (figure 1), however if custom nucleotide(s) are connected and are not phosphorylated at the 3’ position, the conversion incorrectly joins the deoxyriboses to form a peroxide (figure 2).
 


 


 
This has been resolved in release 2018 products (see figure 3): the correct phosphorylation is honored when connecting a custom nucleotide with no phosphate at the 3’ position.
 


 
What you should do
If you believe that you are potentially affected, please contact BIOVIA Support. We’ll need to know:

•         Which of the workflows and product combinations described above you have used
•         What product version(s) you are currently using
•         Where the possibly-compromised sequence data now resides
•         Whether you have Pipeline Pilot and/or Direct (irrespective of whether these feature in the workflows you have used)

Resolution:
This issue has been logged as defect (issue number PCHE-7127) and has been resolved in release 2018 products where the correct phosphorylation is honored when connecting a custom nucleotide with no phosphate at the 3’ position.