SMARTScompareViewer

Overview

The SMARTScompareViewer and the accompanying SMARTScompare  command line tool are the first algorithmic solutions for chemical pattern analysis especially designed for the SMARTS language. SMARTScompare is based on an exhaustive enumeration of SMARTS distinguishable atom states employing the NAOMI chemistry model. The enumerated atom states are converted into fingerprints assigned to all nodes of SMARTS pattern enabling node-wise comparison for similarity and subset relations between SMARTS patterns. The full description of the SMARTScompare algorithm as well as a comprehensive analysis of SMARTS filter patterns can be found in the respective publications (see below). The SMARTScompareViewer offers additional in-depth information about single comparisons in an interactive GUI. The tool visualizes SMARTS patterns as well as the calculated mapping between the nodes.

Software Availability

The SMARTScompareViewer tool is available for Linux, MacOS, and Windows as part of the NAOMI ChemBio Suite at https://uhh.de/naomi and is free for academic use and evaluation purposes.

People and references

For further reading on the new SMARTScompareViewer please see:

Schmidt, R.;  Ehmki, E.S.R.; Ohm, F.;  Ehrlich, H.-C.; Mashzchev, A.;  Rarey, M. (2019): Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. Journal of Chemical Information and Modeling, 59(6), 2560-257
https://pubs.acs.org/doi/10.1021/acs.jcim.9b00250

Ehmki, E.; Schmidt, R.; Ohm, F.; Rarey, M. (2019): Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. Journal of Chemical Information and Modeling, 59(6), 2572-2586
https://pubs.acs.org/doi/10.1021/acs.jcim.9b00249