title: Ambit-Tautomer: An Open Source Tool for Tautomer Generation.
abstract: We present a new open source tool for automatic generation of all tautomeric forms of a given organic compound. Ambit-Tautomer is a part of the open source software package Ambit2. It implements three tautomer generation algorithms: combinatorial method, improved combinatorial method and incremental depth-first search algorithm. All algorithms utilize a set of fully customizable rules for tautomeric transformations. The predefined knowledge base covers 1-3, 1-5 and 1-7 proton tautomeric shifts. Some typical supported tautomerism rules are keto-enol, imin-amin, nitroso-oxime, azo-hydrazone, thioketo-thioenol, thionitroso-thiooxime, amidine-imidine, diazoamino-diazoamino, thioamide-iminothiol and nitrosamine-diazohydroxide. Ambit-Tautomer uses a simple energy based system for tautomer ranking implemented by a set of empirically derived rules. A fine-grained output control is achieved by a set of post-generation filters. We performed an exhaustive comparison of the Ambit-Tautomer Incremental algorithm against several other software packages which offer tautomer generation: ChemAxon Marvin, Molecular Networks MN.TAUTOMER, ACDLabs, CACTVS and the CDK implementation of the algorithm, based on the mobile H atoms listed in the InChI. According to the presented test results, Ambit-Tautomer's performance is either comparable to or better than the competing algorithms. Ambit-Tautomer module is available for download as a Java library, a command line application, a demo web page or OpenTox API compatible Web service.
authors.affiliation: Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tzar Assen Str., Plovdiv 4000, Bulgaria. nick@uni-plovdiv.net.
authors.forename: Nikolay T
authors.initials: NT
authors.lastname: Kochev
authors.affiliation: Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tzar Assen Str., Plovdiv 4000, Bulgaria.
authors.forename: Vesselina H
authors.initials: VH
authors.lastname: Paskaleva
authors.affiliation: Ideaconsult Ltd. 4 A. Kanchev str., Sofia 1000, Bulgaria.
authors.forename: Nina
authors.initials: N
authors.lastname: Jeliazkova
keywords: Depth-first search; Rule-based approach; Substructure search; Tautomer generation; Tautomerism