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SiRMS

Simplex representation of molecular structure (SiRMS) - a chemoinformatic tool for calculation of simplex descriptors.
Simplex - tetraatomic fragment of fixed composition, structure, chirality and symmetry.
Simplex descriptor - the number of identical simplexes in the structure.
Starting from the version 1.0.0 the support of fragments with any number of atoms was added.

Project description

This is an open-source implementation of software which calculates simplex (fragment) descriptors for:

• single compounds
• quasi-mixtures of single compounds
• compound mixtures of any complexity
• chemical reactions

Important notes

1. This version of software calculates only 2D descriptors.
2. Standardization of compounds structures before descriptors calculation is absolutely necessary to obtain reliable results (e.g. Chemaxon Standardizer).

References

1. Kuz’min, V. E.; Artemenko, A. G.; Polischuk, P. G.; Muratov, E. N.; Khromov, A. I.; Liahovskiy, A. V.; Andronati, S. A.; Makan, S. Y. Hierarchic System of QSAR Models (1D-4D) on the Base of Simplex Representation of Molecular Structure - Journal of Molecular Modelling, 2005, 11, 457-467. (basic description)
2. Kuz’min, V. E.; Artemenko, A. G.; Muratov, E. N. Hierarchical QSAR technology based on the Simplex representation of molecular structure - Journal of Computer-Aided Molecular Design, 2008, Volume 22, Issue 6-7, 403-421. (basic description)
3. Kuz’min, V. E.; Artemenko, A. G.; Muratov, E. N.; Polischuk, P. G.; Ognichenko, L. N.; Liahovsky, A. V.; Hromov, A. I.; Varlamova, E. V. Virtual Screening and Molecular Design Based on Hierarchical QSAR Technology - Recent Advances in QSAR Studies, Challenges and Advances in Computational Chemistry and Physics, Volume 8, 2010, 127-176. (old scheme of mixture representation)
4. Mokshyna, E.; Nedostup, V. I.; Polischuk, P. G.; Kuzmin, V. E. ‘Quasi-Mixture’ Descriptors for QSPR Analysis of Molecular Macroscopic Properties. The Critical Properties of Organic Compounds. Molecular Informatics, 2014, Volume 33, 647-654. (quasi-mixture representation)