Ambit-GCM: a Software Tool for Group Contribution Modelling
| Main Authors: | Kochev, Nikolay, Paskaleva, Vesselina, Pukalov, Ognyan, Jeliazkova, Nina |
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| Format: | info software |
| Bahasa: | eng |
| Terbitan: |
, 2018
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/1470793 |
Daftar Isi:
- Ambit-GCM is a software tool for group contribution modelling (GCM), developed as part of the chemoinformatics platform AMBIT [1]. It is an open-source tool distributed under LGPL license, written in Java and relies on the Chemistry Development Kit [2]. It provides an environment for creating models of molecular properties using additive schemes from zero, first or higher orders. Ambit-GCM provides a set of local atomic attributes used for dynamic configuration of desired atom descriptions. Then atom descriptions are used to define fragments of different sizes (atomic groups, bonds, G-groups, D-groups, rings, etc.). 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 user can define correction factors via custom SMARTS notations or add externally calculated molecular descriptors. Molecular property model is obtained as a sum over all found groups multiplying each group or correction factor frequency to its corresponding contribution. Multivariable linear regression analysis (MLRA) is used for group contribution calculation. Ambit-GCM performs full statistical characterization of the obtained MLRA models via various validation techniques: external tests validation, cross validation, y-scrambling etc. In addition, the software can be optionally used only for molecule fragmentation and group calculation and then external statistical modelling package can be applied for further processing. [1] N. Jeliazkova, V. Jeliazkov, J. Cheminform. 2011, 3(1), p.18 [2] ] E.L. Willighagen, J.W. Mayfield, J. Alvarsson, A. Berg, L. Carlsson, N. Jeliazkova, S. Kuhn, T. Pluskal, M. Rojas-Chertó, O. Spjuth, G. Torrance, C.T. Evelo, R. Guha, C. Steinbeck, J. Cheminform, 2017, 9(1), 33.
- gcm-v1.1.jar is used for model creation gcm-predict-v1.1.jar is used for molecular property prediction on the base of already created GCM models. More detailed information and usage examples are given in file GCM-usage-examples.pdf and data-files.zip Source code of Ambit-GCM is available as part of Ambit (http://ambit.sourceforge.net/)