Reaction Representation and Structure Transformation with Ambit-SMIRKS.
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Best poster award at http://www.opentox.org/meet/opentoxeu2013/opentoxeuro13awards ...
Best poster award at http://www.opentox.org/meet/opentoxeu2013/opentoxeuro13awards
7. Reaction Representation and Structure Transformation with Ambit-SMIRKS. Application in Metabolite prediction
Ambit-SMIRKS is a new extension of the Ambit-SMARTS Java library , both part of the Ambit2  project. The modules are implemented on top of the Chemistry Development Kit (CDK) . Ambit-SMIRKS performs two main tasks: (1) parsing of SMIRKS linear notations into internal reaction (transformation) representations based on CDK objects and (2) application of the stored reactions against target molecules for actual transformation of the target chemical objects. The transformations can be applied on various sites of the target molecule in several modes: single, non-overlapping, non-identical, non-homomorphic or externally specified list of sites. Ambit-SMARTS implements the entire SMARTS language specification as defined by Daylight, plus additional syntax extensions to make software compliant with SMARTS modifications made by third party software packages such as OpenEye, MOE and OpenBabel. The SMIRKS library utilizes the SMARTS parser and the efficient substructure searching algorithm implemented within Ambit-SMARTS package . Typically most SMIRKS implementations support SMILES plus simple SMARTS syntax features. However, Ambit-SMIRKS module supports full SMARTS syntax for reactions specification. The SMIRKS module is used to enable metabolite predictions in Toxtree (since version 2.5.0) , once the site of metabolism is predicted by SMARTCyp . Toxtree is a flexible and user-friendly open-source application that predicts various kinds of toxic effects, mostly by applying structural alerts, arranged in a decision tree fashion. SMARTCyp (Cytochrome P450-Mediated Drug Metabolism) model is originally developed by Patrik Rydberg et al  and was included as Toxtree module since Toxtree 2.1.0. Ambit-SMIRKS functionality is available as a Java library as well as OpenTox Algorithm API compatible Web service. We also welcome testing the SMIRKS at the web page http://apps.ideaconsult.net:8080/ambit2/depict/reaction.
 N. Jeliazkova, N. Kochev, AMBIT-SMARTS: Efficient Searching of Chemical Structures and Fragments, Mol. Inf., 30: 707–720, 2011
 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.
 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
 P. Rydberg, D. Gloriam, J. Zaretzki, C. Breneman, L. Olsen, SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism
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