Hi all, I have a question regarding the expected topological connectivity of the compounds in the DEL library. Based on standard tri-building block DEL synthesis designs, the assumption is often that BB1 serves as a scaffold, BB2 acts as a linker/core reacting with BB1, and BB3 subsequently reacts with BB2—resulting in a linear BB1–BB2–BB3 connection pattern. However, reviewing the example diagram on the challenge wiki ([DEL Synthesis - Important concepts](https://www.synapse.org/Synapse:syn75349604/wiki/641133)), BB3 appears to react directly with BB1 rather than BB2. Could you clarify the connectivity rules across the dataset? Specifically: 1. Are BB1 and BB3 strictly separated by BB2 in all library members, or are there sub-libraries/reaction schemes where BB3 connects directly to BB1? 2. Should we rely exclusively on the enumerated SMILES to establish connectivity, or does the wiki diagram reflect a specific alternative topology present in the library? Thanks in advance for your guidance!

Created by João Pedro Aroucha jparoucha
Hi jparoucha, The image in the (DEL Synthesis - Important concepts) images is one example of possible building block topologies. We do have DELs that were built BB1:BB2:BB3, where the :s indicate which BBs are bonded to which. Hit *names* are given as BB1-BB2-BB2, where BBn is a number or other token, but these dashes do NOT indicate which BB is bonded to which, merely the order in which the chemistry was done. Hit BB1-BB2-BB3 from qDOS11 is actually assembled as: BB2:BB1:BB3 BB1 is ALWAYS attached the DNA headpiece (in the first reaction), but some libraries are branched and some are linear. The SMILES associated with a BB1-BB2-BB3 *name* should be the product that results from correctly assembling the BBs as determined by the way the chemistry was done (i.e., branched or linear). You can't always trust a smile, but please trust the SMILES. If you want to use BB information independent of the final SMILES, and you think you could use more info, please ask. cheers...

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