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Ambit‐Tautomer: An Open Source Tool for Tautomer Generation

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.