Ambit-GCM: An Open-source Software Tool for Group Contribution Modelling

Ambit-GCM is a new software tool for group contribution modelling (GCM), developed as a part of the chemoinformatics platform AMBIT. It is an open-source tool distributed under LGPL license, written in Java and based on the Chemistry Development Kit. Ambit-GCM provides an environment for creating models of molecular properties using additive schemes of zero, first or second orders. Ambit-GCM supports a set of local atomic attributes used for dynamic configuration of desired atom descriptions, which are applied to define fragments of different sizes. All defined groups are exhaustively generated for each molecule from a training set of compounds and combined to form the basic set of GCM fragments. Additionally, Ambit-GCM users can define correction factors via custom SMARTS notations or add externally calculated molecular descriptors. A molecular property model is obtained as a sum over all found groups by multiplying each group or correction factor frequency to its corresponding contribution. Multiple linear regression analysis (MLRA) is used for group contributions calculation. Ambit-GCM performs full statistical characterization of the obtained MLRA models via various validation techniques: external tests validation, cross validation, y-scrambling, etc. The software can be optionally used only for molecule fragmentation combined with an external statistical modelling package for further processing. Ambit-GCM example usage and test cases are given.