SlideShare is now on Android. 15 million presentations at your fingertips.  Get the app

×
  • Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
 

ALGORITHMS FOR AUTOMATIC TAUTOMER GENERATION AND THEIR APPLICATIONS

by Working at http://www.ideaconsult.net on Oct 22, 2013

  • 124 views

OpenTox Euro 2013 poster ...

OpenTox Euro 2013 poster
http://www.opentox.org/meet/opentoxeu2013/opentoxeu2013posters/

6. Ambit-TAUTOMER – a Software Tool for Automatic Tautomer Generation, Nina Jeliazkova (Ideaconsult Ltd)
Ambit-Tautomer [1] is an open source Java library for automatic generation of all tautomers of a given chemical compound. It is implemented on top of the Chemistry Development Kit (CDK) [2]. The system includes three main algorithms: pure combinatorial method, improved combinatorial method and incremental algorithm. The tautomer generator uses a set of predefined, but customizable rules. The rules are defined by Daylight SMILES/SMARTS line notations and support the basic types of tautomerism (1-3, 1-5 and 1-7 proton tautomer shifts). The pure combinatorial method generates all tautomeric forms considering all possible combinations of the matched rule states. The improved combinatorial method uses sub-combinations based on rules clustering. The incremental algorithm applies depth-first search to handle sophisticated cases of overlapping rules. Additionally, rule pre-filtering and tautomer post-filtering are applied for fine tuning of the generation process. The tautomer generator implements tautomer ranking based on empirical rules defined in terms of relative energy difference. Ambit-Tautomer library is applied to improve the Ambit database storage of chemical structures and accordingly to implement search procedures which take into account the tautomerism information. Also the tautomer sets are used to calculate modified values of the original molecular descriptors in order to improve existing QSAR/QSPR models. Ambit-Tautomer module is implemented as open source Java package as part of the Ambit open source software for chemoinformatics and data management [3,4] and is available as a Java library, command line application [5] and OpenTox Algorithm API compatible Web service [6]. Ambit package is available as online web services and as a downloadable application. A web page providing online tautomer generation by Ambit-Tautomer and several different software packages is available on http://apps.ideaconsult.net:8080/ambit2/depict/tautomer.

References
[1] Kochev, N. T., Paskaleva, V. H. and Jeliazkova, N., Ambit-Tautomer: An Open Source Tool for Tautomer Generation. Mol. Inf., 32: 481–504, 2013
[2] C. Steinbeck, Y. Han, S. Kuhn, O. Horlacher, E. Luttmann, E. Willighagen, The Chemistry Development Kit (CDK):  An Open-Source Java Library for Chemo- and Bioinformatics, J. Chem. Inf. Comput. Sci., 43: 493–500, 2003
[3] Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface, Journal of Cheminformatics 2011, 3:18, doi:10.1186/1758-2946-3-18.
[4] http://ambit.sourceforge.net
[5] https://github.com/ideaconsult/examples-ambit/tree/master/tautomers-example
[6] http://apps.ideaconsult.net:8080/ambit2/algorithm/tautomers

Statistics

Views

Total Views
124
Views on SlideShare
124
Embed Views
0

Actions

Likes
0
Downloads
2
Comments
0

0 Embeds 0

No embeds

Accessibility

Categories

Upload Details

Uploaded via SlideShare as Adobe PDF

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
Post Comment
Edit your comment

ALGORITHMS FOR AUTOMATIC TAUTOMER GENERATION AND THEIR  APPLICATIONS ALGORITHMS FOR AUTOMATIC TAUTOMER GENERATION AND THEIR APPLICATIONS Document Transcript