What is a powerful software for analyzing several databases of compounds in .sdf format to find overlaps?

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Stanislav Geidl

Generate INCHI or INCHI key for every compound and compare it.

Ahmed Mohamed

As already suggested, R is exactly what you need. I would use Chemminer package. See the link here for the installation and usage manual. https://bioconductor.org/packages/release/bioc/html/ChemmineR.html

Pavlína Cicková

Thanks, I was actually thinking exactly about Chemminer package in R. I was just wondering if there is maybe not something even more suitable that I don't know.