Downloads:
- Windows setup (Java Runtime Environment NOT included)
- AmbitDiscovery-v0.04-online-setup.exe
- Windows setup (Java Runtime Environment 1.4 included)
- AmbitDiscovery-v0.04-offline-setup.exe
- Zip archive (platform independent)
- AmbitDiscovery-v0.04.zip
AMBIT Discovery is an user-friendly open source application, which estimates applicability domain of QSAR models by assessing structural similarity to a set of chemicals. It calculates the similarity of a chemical to a set in the following ways. The first approach is based on distances (Euclidean, City block) suitable when similarity is assessed in descriptors space. Several preprocessing data functionalities are available to deal with linearly dependent descriptors (rotation via Principal Component Analysis), centering to remove effects of different numerical values ranges of the descriptors before PCA.
AMBIT Discovery provides means to calculate the probability of a chemical belonging to a set represented by non-parametric probability density estimation. To assess structural similarity the user has a choice of Daylight style hashed fingerprints or atom environments (topological neighborhood). Details on similarity methods are provided in:
Publication
- Jaworska 2007
- Joanna Jaworska, Nina Nikolova-Jeliazkova, How can structural similarity analysis help in category formation, SAR and QSAR in Environmental Research, vol 18, 3-4 ( 2007)