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Because the linking subtypes are explicitly restricted by smiles (atoms with implicit hydrogens) and the linker_labels. A new subtype needs to be created for a different type of linking.
To have a distinguishable subtype name, the 5' to 3' notation needs to include:
p <-- phosphate, if any
5' <-- intramol linker position to phosphate
DA <-- type of base name
3' <-- linker position to next nucleotide
p5'DA3' will be the standard embedded form of Adenosine in DNA. A short sequence may consist of:
(5'DT3') - (p5'DA3') - (p5'DC3') - (p5'DG3')
Currently they're named:
(DT5) - (DA) - (DC) - (DG3)
The text was updated successfully, but these errors were encountered:
rwxayheee
changed the title
X5p can have a unique residue name
X3p can have a unique residue name
Oct 7, 2024
rwxayheee
changed the title
X3p can have a unique residue name
Linking subtypes are explicitly restricted by smiles and linker_labels in chem templates
Oct 14, 2024
Because the linking subtypes are explicitly restricted by smiles (atoms with implicit hydrogens) and the linker_labels. A new subtype needs to be created for a different type of linking.
To have a distinguishable subtype name, the 5' to 3' notation needs to include:
p <-- phosphate, if any
5' <-- intramol linker position to phosphate
DA <-- type of base name
3' <-- linker position to next nucleotide
p5'DA3' will be the standard embedded form of Adenosine in DNA. A short sequence may consist of:
(5'DT3') - (p5'DA3') - (p5'DC3') - (p5'DG3')
Currently they're named:
(DT5) - (DA) - (DC) - (DG3)
The text was updated successfully, but these errors were encountered: