6.1: Molecular Descriptors - Chemistry LibreTexts
Jul 26, 2022 · The PubChem fingerprint is a 881-bit-long structural key, which is used by PubChem for similarity searching (interactively through the PubChem Homepage or programmatically through PUG-REST). It is also used for structure neighboring, which “pre-computes” a list of similar chemical structure for each compound.
The PubChem Compound Help
Similarity is measured using the Tanimoto equation and the PubChem dictionary-based binary fingerprint. This fingerprint consists of series of chemical substructure "keys". Each key denotes the presence or absence of a particular substructure in a molecule. The fingerprint does not consider variation in stereochemical or isotopic information.
Docs - PubChem
PubChem Data Specification, PubChem Fingerprint Description, & PubChem SD Fields Description.
6.5: R Assignment - Chemistry LibreTexts
Jul 26, 2022 · The PubChem Fingerprint is a 881-bit-long binary fingerprint (ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf). Similar to the MACCS keys, it uses a pre-defined fragment dictionary.
Data Specification - PubChem
PubChem Data Specification, PubChem Fingerprint Description, & PubChem SD Fields Description.
6.4: Python Assignment - Chemistry LibreTexts
Jul 26, 2022 · The PubChem Fingerprint is a 881-bit-long binary fingerprint (ftp://ftp.ncbi.nlm.nih.gov/pubchem/s...ngerprints.pdf). Similar to the MACCS keys, it uses a pre-defined fragment dictionary. The PubChem fingerprint for each compound in PubChem can be downloaded from PubChem.
Generate fingerprint files from PubChem SD tags
chemfp implements two platform-independent fingerprints where were originally designed for substructure filters but which are also used for similarity searches. One is based on the 166-bit MACCS implementation in RDKit and the other comes from the 881-bit PubChem/CACTVS substructure fingerprints.
Molecular fingerprint similarity search in virtual screening
Jan 1, 2015 · PubChem fingerprint [12]: this fingerprint, with 881 structural keys covers a wide range of different substructures and features. It is the fingerprint used by PubChem for similarity searching and neighboring.
deepchem/deepchem/feat/molecule_featurizers/pubchem_fingerprint…
PubChemPy use REST API to get the fingerprint, so you need the internet access.
Chemical fingerprints and similarity.ipynb - GitHub
Python wrapper for the PubChem PUG REST API. Contribute to mcs07/PubChemPy development by creating an account on GitHub.