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Ambit-Tautomer: An Open Source Tool for Tautomer Generation.

Nikolay T Kochev1, Vesselina H Paskaleva2, Nina Jeliazkova3

  • 1Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tzar Assen Str., Plovdiv 4000, Bulgaria. nick@uni-plovdiv.net.

Molecular Informatics
|August 3, 2016
PubMed
Summary

Ambit-Tautomer is a new open-source tool for generating all tautomeric forms of organic compounds. Its performance is comparable to or better than existing software, offering customizable rules and multiple access points.

Keywords:
Depth-first searchRule-based approachSubstructure searchTautomer generationTautomerism

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Area of Science:

  • Computational chemistry
  • Cheminformatics
  • Software development

Background:

  • Tautomerism is crucial in organic chemistry, influencing compound properties and reactivity.
  • Accurate generation of tautomeric forms is essential for chemical databases and drug discovery.
  • Existing software for tautomer generation has limitations in scope or performance.

Purpose of the Study:

  • To introduce Ambit-Tautomer, a novel open-source tool for the automatic generation of all tautomeric forms of organic compounds.
  • To implement and compare multiple tautomer generation algorithms within a single framework.
  • To provide a flexible and high-performing solution for tautomer enumeration.

Main Methods:

  • Implementation of three tautomer generation algorithms: combinatorial, improved combinatorial, and incremental depth-first search.
  • Utilization of a customizable rule set for tautomeric transformations, including 1-3, 1-5, and 1-7 proton shifts.
  • Development of an energy-based ranking system and post-generation filters for output control.

Main Results:

  • Ambit-Tautomer successfully generates diverse tautomeric forms, supporting common tautomerism rules like keto-enol and imin-amin.
  • Exhaustive comparison demonstrated Ambit-Tautomer's performance to be comparable or superior to leading commercial and open-source software.
  • The tool offers flexible access via Java library, command-line application, web demo, and OpenTox API.

Conclusions:

  • Ambit-Tautomer provides a robust, efficient, and versatile solution for tautomer generation in computational chemistry.
  • The open-source nature and multiple access points facilitate its integration into various research workflows.
  • This tool enhances the capability for accurate chemical structure representation and analysis.