Ambit-SMIRKS
Ambit-SMIRKS is an extension of the AMBIT-SMARTS Java library, both part of the AMBIT project, it is used to enable:
- metabolite predictions in Toxtree SMARTCyp module, once that site of metabolisms are predicted by SMARTCyp
- structure transformation for the purpose of chemical structure standardisation
- Biotransformation predictions in enviPath
- BioTransformer a tool developed by The human metabolome database (HMDB 4.0) team.
- Ambit Reactor
Main functionality
- Parsing of SMIRKS linear notations into internal reaction (transformation) representations based on The Chemistry Development Kit objects
- Application of the stored reactions against target molecules for actual transformation of the target chemical objects
Transformation mapping modes
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
Maven artifacts
- Depends on The CDK 1.5.13
<dependency>
<groupId>ambit</groupId>
<artifactId>ambit2-smarts</artifactId>
<version>3.1.0-SNAPSHOT</version>
</dependency>
<repository>
<id>nexus-idea-snapshots</id>
<url>https://nexus.ideaconsult.net/content/repositories/snapshots</url>
</repository>
- Depends on The CDK 1.5.10
<dependency>
<groupId>ambit</groupId>
<artifactId>ambit2-smarts</artifactId>
<version>3.0.0</version>
</dependency>
<repository>
<id>nexus-idea-releases</id>
<url>https://nexus.ideaconsult.net/content/repositories/releases</url>
</repository>
Code examples
IAtomContainer target = (initialize)
SMIRKSManager smrkMan = new SMIRKSManager();
SMIRKSReaction reaction = smrkMan.parse(smirks);
if (!smrkMan.getErrors().equals("")) {
throw(new Exception("Smirks Parser errors:\n" + smrkMan.getErrors()));
}
if (smrkMan.applyTransformation(target, reaction))
return target; //all products inside the same atomcontainer, could be disconnected
else return null;
- Generate separate products for every possible reaction (used in Toxtree)
SMIRKSManager smrkMan = new SMIRKSManager();
SMIRKSReaction smr = smrkMan.parse(reaction.getSMIRKS());
IAtomContainer product = reactant; //(IAtomContainer) reactant.clone();
IAtomContainerSet rproducts = smrkMan.applyTransformationWithSingleCopyForEachPos(product, null, smr);
//products returned in a separate atom sontainer set
Applications
Toxtree
Toxtree is an open-source application that predicts various kinds of toxic effects, mostly by applying structural alerts, arranged in a decision tree fashion. You could download the application or test Toxtree online
enviPath - The environmental contaminant biotransformation pathway resource
To represent the biotransformation rules, enviPath use SMIRKS. enviPath uses AMBIT-SMARTS, which implements SMARTS and SMIRKS for CDK.
-
Wicker, J.; Lorsbach, T.; Gutlein, M.; Schmid, E.; Latino, D.; Kramer, S.; Fenner, K. enviPath - The environmental contaminant biotransformation pathway resource. Nucleic Acids Res. 2016 DOI: 10.1093/nar/gkv1229.
Ambit SMIRKS applications
Publications
-
Best poster award at OpenTox Euro 2013
-
AMBIT SMARTS Publication N. Jeliazkova and N. Kochev, AMBIT-SMARTS: Efficient Searching of Chemical Structures and Fragments, Mol. Inform., vol. 30, no. 8, pp. 707-720, 2011.