Similarity Search with Open Babel

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Similarity Search with Open Babel

This chapter provides introductions and tutorial examples on Open Babel 'obabel ... -o fpt' command to do molecule similarity search. Topics include performing similarity search; generating different types of molecule fingerprints; displaying fingerprint ragments.

These sections are omitted from this Web preview version. To view the full content, see information on how to obtain the full version this book.

"obabel ... -o fpt" Command - Similarity Search

"obabel ... -o fpt" Similarity Search for Substructure Search

"obabel ... -o fpt -xf..." Use Different Fingerprints

Generate Fingerprint of a Single Molecule

What Is Tanimoto Coefficient

obabel ... -ofpt -xs" - Display Fingerprint Fragments

FP2 Exhaustive Fingerprint Fragments with Open Babel

FP2 Fingerprint Fragment Ends in Ring

"obabel -H fpt" - Fingerprint Help Information

Takeaways:

Open Babel "obabel ... -o fpt" command performs molecule similarity search by comparing molecules fingerprints.
Open Babel uses Tanimoto coefficient molecule fingerprints of two molecules to determine their similarity score.
Open Babel supports multiple fingerprint types: ECFP0, ECFP10, ECFP2, ECFP4, ECFP6, ECFP8, FP2, FP3, FP4, MACCS.
Open Babel's default fingerprint type is FP2, which is limited only up to 7 atoms in linear segments.