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. 2019 Dec 8;21(6):2066–2083. doi: 10.1093/bib/bbz144

Table 4.

Chemoinformatics software to analyze molecular descriptors and fingerprints

Software Descriptions Link References
CDK Open-source modular Java libraries for chemoinformatics https://sourceforge.net/projects/cdk [156]
rcdk R interface to CDK https://cran.r-project.org/web/packages/rcdk [157]
ChemmineR Chemoinformatics package for analyzing drug-like small molecule data in R https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html [158]
Open Babel Support for more than 100 chemical file formats, fingerprint generation, property determination, similarity and substructure search, structure generation and molecular force fields. Available in C++ with Python, Perl, Java, Ruby, R, etc. http://openbabel.org [69]
Mordred 1825 descriptors based on RDKit https://github.com/mordred-descriptor [159]
RDKit Major chemoinformatics tool with capability of handling of molecular data, fingerprints, substructure and similarity search and many other functions http://www.rdkit.org
PaDEL 1875 descriptors (1444 1D and 2D descriptors and 431 3D descriptors) and 12 types of fingerprints (total 16 092 bits) http://www.yapcwsoft.com/dd/padeldescriptor/ [160]
KNIME Graphic development environment that has plugins for chemoinformatics (CDK, RDKit, etc.) and ML modules https://www.knime.org [161, 162]
PubChem Fingerprints of 881 bits in length for 2D structures ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt [80–83]

Descriptions of more chemoinformatics tools can be found in [163, 164].