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I think Using InChI's Main Layer, Charge Layer and Stereochemical layer (InChI String), We can still compare the chemical molecules Structure search (Similarity and Substructure search), But why do most of the applications go for chemical fingerprints for doing similarity search or sub-structure search. What is missing in InChI that is available over a chemical fingerprint (like a daylight or any other fingerprint)

Egon Willighagen
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Wiki
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InChI is great for exact matches, or exact up to a certain level, e.g. without the hydrogen layer you will find all tautomers.

Fingerprints are designed for finding similar molecules. There's no information missing from an InChI but similar molecules can have very different InChI strings.

Egon Willighagen
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chrishmorris
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