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If the query chain has a four-digit classification number in SCOPe and has bound template with the same Homology Indexing in template database, the binding site of this query chain will be detected as the following procedure.
The detection of binding site is based on the bound template (PDB ID: 1oxr, CHAIN ID: A, black) by mapping the ligand of template into unbound chain.
If the query chain has no satisfactory homologous bound template, the binding site of this query chain will be detected as the following procedure.
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Since there are still lots of protein chains have no satisfactory bound structures, bound templates is borrowed for detecting the binding sites in this situation.
Our templates database contains 101,315 bound templates.
Finally, 101,315 chains were obtained for building the database of bound templates.
Then enter the process as the description above (Part 2 of "Workflow of binding sites detection") with top 20 most similar bound templates.
It means that only about 24 (101,315/4254) bound templates are needed to do the time-consuming structural alignment with the query per prediction.
However, the 2 × 1 oligonucleotide induced a significant difference in cleavage between wild-type and mutant templates (p < 0.05), while maintaining no significant difference between the wild-type/2 × 1 and the wild-type complementary bound templates (p > 0.05).
The latter bound RNA template and showed RdRp activity as detected by the incorporation of radiolabel into a neosynthesized RNA strand (Tan et al., 1996).
The constraints were matched against the knowledge base in order to bind template variables to concepts in the knowledge base and thus generate a question.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com