AMBIT:Chemical Structure DB&Web Service Files

AmbitDiscovery is an user-friendly open source application, which estimates applicability domain of QSAR models by various methods. 

SYSTEM REQUIREMENTS & INSTALLATION

AmbitDiscovery requires Java(TM) 2 Runtime Environment, Standard Edition 1.4 or newer on the target system and it is platform-independent. It runs under any host operating system, which supports Java(TM) 2 Runtime Environment, Standard Edition. 

The AmbitDiscovery application is distributed with fully automated online/offline installers (AmbitDiscovery-vX.YZ-online-setup.exe and AmbitDiscovery-vX.YZ-offline- setup.exe), compatible with recent versions of the Microsoft Windows operating system. 

In order to install AmbitDiscovery just run one of the installers and follow its instructions.

The offline installer (AmbitDiscovery-vX.YZ-offline-setup.exe) contains all the required packages, including the Java(TM) 2 Runtime Environment, Standard Edition 1.4 setup.

The online installer (AmbitDiscovery-vX.YZ-online- setup.exe) is much smaller in size and is able to download the Java(TM) 2 Runtime Environment, Standard Edition 1.4 setup from Internet only if needed (in this case the target system should be connected to Internet).

Zip package provides the same content as the installers, but without automatic setup. It is platform independent and can be used to run AmbitDiscovery on different operating systems.
Ambit Discovery is a software tool for assessing structural similarity to a set of chemicals, and for applicability domain assessments. 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. In Ambit Discovery there is also a 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).