Ambit‐Tautomer: An Open Source Tool for Tautomer Generation

Kochev, Nikolay; Paskaleva, Vesselina; Jeliazkova, Nina

doi:10.1002/minf.201200133

Cited by 41 publications

(38 citation statements)

References 26 publications

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“…A number of such tools were initially developed using older versions of the CDK and are updated to new releases as they are made available. Examples include Bioclipse [27, 28] and AMBIT [29–31]. The CDK has also played a role in a number of chemical studies, such as finding the maximally bridging rings in chemical structures [32], prediction of organic reactions [33], and bioactivities of compounds [34].…”

Section: Introductionmentioning

confidence: 99%

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Mayfield²,

et al. 2017

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Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.Results We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.ConclusionsThis paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.Graphical abstractCDK 2.0 provides new features and improved performance Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-017-0220-4) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Mayfield²,

et al. 2017

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“…The presented tool is mainly based on RDKit and it also includes Indigo and ChemAxon for tautomer and stereoisomer enumeration respectively to take into account the pH effect on protonation state and the enumeration of undefined stereocenters. Moreover, additional software are provided in the workflow for non‐academic users (Ambit Tautomer Generator and Vernalis Speedy SMILES Enumerate Stereoisomers nodes). The workflow was only tested on Linux, but can be installed on other operating systems (Windows and MacOS) due to the cross platform development of implemented tools.…”

Section: Resultsmentioning

confidence: 99%

“…It is noteworthy that OpenEye and ChemAxon, under specific terms and conditions, offer free use of their software to academics. Free toolkits are also available such as Open Babel, CDK, RDKit, Indigo, NAOMI (UNICON) and others . Tools freely available to academics can be combined with other toolkits in a general framework of computational processes in order to improve efficiency .…”

Section: Introductionmentioning

confidence: 99%

VSPrep: A General KNIME Workflow for the Preparation of Molecules for Virtual Screening

Gally

Bourg

Do³

et al. 2017

Molecular Informatics

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Over the past decades, virtual screening has proved itself to be a valuable asset to identify new bioactive compounds. The vast majority of commonly used techniques can be described in three steps: pre-processing the dataset i. e. small (ligands) and eventually larger (receptors) molecules, execute the method and finally analyse the results. Hence, the preparation of ligands is a critical step for success of commonly used virtual screening approaches such as protein-ligand docking, similarity or pharmacophore search. We present here a new workflow, VSPrep, for the pre-processing of small molecules; it is based on freely accessible tools for academics and is integrated within the KNIME platform. It can be used to perform several chemoinformatics tasks such as molecular database cleaning, tautomer and stereoisomer enumeration, focused library design and conformer generation. Additionally, graphical reports of the results are provided to the user as a convenient analysis tool.

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“…17 Tautomeric analysis has been carried out using the Ambit-tautomer program. 18 3. Results and discussion 3.1.…”

Section: Computational Detailsmentioning

confidence: 99%

The influence of intermolecular halogen bonds on the tautomerism of nucleobases. I. Guanine

2015

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Ambit‐Tautomer: An Open Source Tool for Tautomer Generation

Cited by 41 publications

References 26 publications

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

VSPrep: A General KNIME Workflow for the Preparation of Molecules for Virtual Screening

The influence of intermolecular halogen bonds on the tautomerism of nucleobases. I. Guanine

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