GraphSim TK
GraphSim TK is an important part of the OpenEye cheminformatics suite of toolkits built on top of OEChem. It provides five different fingerprint types to perform 2D molecular similarity measurements: MACCS key, LINGO [1,2], and highly customizable implementations of path, circular, and tree fingerprints. Users are allowed to set the fingerprint size as well as various atom/bond types, and can specify the length of the enumerated paths. Six common similarity indices (Cosine, Dice, Euclidean, Manhattan, Tanimoto, Tversky) are available, while user-defined similarity measures are also applicable.
Figure 1: Example of enumerating all circular fragments with one radius
Figure 2: Example of enumerating all unique tree fragments with four bonds
References
- LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, D. Vida, M. Thormann and M. Pons. J. Chem. Inf. Model., 2005, 45 (2), pp 386-393
- Lingos, Finite State Machines, and Fast Similarity Searching J.A. Grant, J.A. Haigh, B.T. Pickup, A. Nicholls and R.A. Sayle. J. Chem. Info. Model., 2006, 46 (5), pp 1912-1918
