Molecular fingerprints and similarity searching — Open Babel v2.3.0 documentation

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# Molecular fingerprints and similarity searching

Molecular fingerprints are a way of encoding the structure of a molecule. The most common type of fingerprint is a series of binary digits (bits) that represent the presence or absence of particular substructures in the molecule. Comparing fingerprints allows you to determine the similarity between two molecules, to find matches to a query substructure, etc.

Open Babel provides several fingerprints of different types:

- Fingerprint format: the path-based fingerprint FP2; substructure based fingerprints FP3, FP4 and MACCS; user-defined substructures
- Multilevel Neighborhoods of Atoms (MNA) (mna): a circular fingerprint
- MolPrint2D format (mpd): a circular fingerprint
- Spectrophores™: a fingerprint that encodes the 3D structure of a molecule

The next two sections describe the Fingerprint format and Spectrophores in depth. For the others, see the relevant sections listed above.

- Fingerprint format
  - Similarity searching
    - Small datasets
    - Large datasets
  - Substructure searching
    - Small datasets
    - Large datasets
  - Case study: Search ChEMBLdb
- Spectrophores™
  - Introduction
  - obspectrophore
  - Implementation
    - Atomic properties
    - Interaction between the atoms and cage points
  - Choice of Parameters
    - Accuracy
    - Resolution
    - Stereospecificity
    - Normalisation

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