| RDKit [127] |
Descriptor and fingerprint generation for machine learning; molecular database cartridge for PostgreSQL; supporting substructure and similarity searches as well as various descriptor calculators; automatic feature perception (i.e. rings, bonds, hybridization and aromaticity) Supported file formats: SMILES, SMARTS and InChI
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Microsoft Windows, Linux, Mac OSX |
Python; wrappers are available for Java and C# |
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| OpenBabel [128] |
Filtering and searching molecular files; converting files, molecular searching, chirality detection and superimposing molecules; Gasteiger–Marsili partial charge calculation; support for molecular mechanics; hydrogen addition and deletion; isotope support, calculation of average and exact masses; automatic feature perception (rings, bonds, hybridization and aromaticity) Supported file formats: mol2, PDB and SMILES
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Microsoft Windows, Linux, Mac OSX |
C++, Perl, Python interfaces |
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| Dragon [129] |
Calculation of molecular descriptors; graphical interface for selection of structures; providing graphics and statistics tools; preliminary descriptor analysis such as the analysis of molecule distribution in the descriptor space, as well as a preliminary correlation analysis; a molecule viewer to display the molecular structures; principal component analysis implementation for the selected sets of descriptors Supported file formats: SMILES, MDL, Sybyl
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Microsoft Windows, Linux |
Stand-alone application |
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| DayLight Tookit [130] |
Subgraph pattern matching; analyzing and manipulate 2D and 3D data; creating new fingerprints; specifying size and folding parameters for a fingerprint; manipulating fingerprints in a bitwise fashion; creating new similarity metrics with mathematical expressions Supported file formats: SMILES and SMARTS
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Microsoft Windows, Linux, Solaris |
C, Fortran; Wrappers are available for Java and C++ |
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| Chemistry Development Tookit [131] |
Interconversion between different types of representations; similarity calculation between two compounds; searching substructures using SMARTS; rendering chemical structures; algorithms for chemical graph theory; 3D conformer generation; various types of fingerprint calculation; generation of QSAR descriptors Supported file formats: SMILES, SMARTS, InChI, etc.
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Microsoft Windows, Linux, MacOSX |
Java |
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| Open Eye Toolkit [132] |
Real-time shape similarity for VS, lead hopping and shape clustering; molecule rendering and depiction; 2D molecular similarity calculation based on fingerprints; molecular property calculation and filtering; molecular docking and scoring; 3D conformer generation and superimposition. Supported file formats: SMILES, InChI, RDF, etc.
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Microsoft Windows, Linux, MacOSX |
C++; Wrappers are available for Python, Java, and.NET |
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| ChemmineR [133] |
Format Interconversions; similarity searching using various criteria such as atom pairs, PubChem fingerprints etc.; rendering chemical structure images; providing various types of clustering algorithms; searching PubChem database using various criteria such as Id, SMILES, etc.; and visualization functions for compound clustering Supported file formats: InChI, SMILES, SDF
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Microsoft Windows, Linux, MacOSX |
R |
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| Indigo [134] |
Exact matching, substructure matching, SMARTS matching; molecule fingerprinting, molecule similarity computation; molecular weight and molecular formula computation; combinatorial chemistry scripts; renderer plugin distributed together with the Indigo API Supported file formats: SMILES, SMARTS, RDF, etc.
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Microsoft Windows, Linux, MacOSX |
C++; Java, Python, Wrapper is available for .NET |
