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] |