Tautomerism in chemical information management systems

Warr, Wendy A.

doi:10.1007/s10822-010-9338-4

Cited by 45 publications

(40 citation statements)

References 25 publications

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“…In this, Wendy Warr [19] outlined the various approaches taken by 27 software vendors and database providers to treat tautomers. There is still no consensus on whether tautomers should be canonicalised and if so how it is done.…”

Section: Business Rules For Standardisationmentioning

confidence: 99%

Chemical databases: curation or integration by user-defined equivalence?

Hersey

Chambers

Bellis

et al. 2015

Drug Discovery Today: Technologies

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There is a wealth of valuable chemical information in publicly available databases for use by scientists undertaking drug discovery. However finite curation resource, limitations of chemical structure software and differences in individual database applications mean that exact chemical structure equivalence between databases is unlikely to ever be a reality. The ability to identify compound equivalence has been made significantly easier by the use of the International Chemical Identifier (InChI), a non-proprietary line-notation for describing a chemical structure. More importantly, advances in methods to identify compounds that are the same at various levels of similarity, such as those containing the same parent component or having the same connectivity, are now enabling related compounds to be linked between databases where the structure matches are not exact.

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Section: Business Rules For Standardisationmentioning

confidence: 99%

Chemical databases: curation or integration by user-defined equivalence?

Hersey

Chambers

Bellis

et al. 2015

Drug Discovery Today: Technologies

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“…[21] Sayle [20] addressed particularly the problems that arise with automated tautomer generation. He has identified five types of tautomer problems:C omparison, Canonicalization, Enumeration, Selection, and Prediction.…”

Section: Existing Tautomer Generating Algorithms and Softwarementioning

confidence: 99%

A Branch‐and‐Bound Approach for Tautomer Enumeration

Thalheim

Wagner

Kühne

et al. 2015

Molecular Informatics

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Knowledge about tautomer forms of a structure is important since, e.g., a property prediction for a molecule can yield to different results which depend on the individual tautomer. Tautomers are isomers that can be transformed to each other through chemical equilibrium reactions. In this paper the first exact Branch‐and‐Bound (B&B) algorithm to calculate tautomer structures is proposed. The algorithm is complete in the sense of tautomerism and generates all possible tautomers of a structure according to the tautomer definition, it is initialized with. To be efficient, the algorithm takes advantage of symmetric and formation properties. Some restrictions are used to enable an early pruning of some branches of the B&B tree. This is important, since a simple enumeration strategy would lead to number of candidate tautomers that is exponentially increasing with the number of hydrogen atoms and their attachment sites. The proposed implementation of the B&B algorithm covers the majority of the prototropic tautomer cases, but can be adapted to other kinds of tautomerism too. Furthermore, a computer processable definition of tautomerism is given in the form of the moving hydrogen atom problem.

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“…An overview of software packages dealing with various problems regarding tautomers and their representation was given by Warr [259]. Despite the mentioned publications about protonation and tautomers in drug design, remarkably few publications deal with the problem of protomeric and tautomeric states in docking.…”

Section: Influence Of Ph and Protonation States In Docking Studiesmentioning

confidence: 99%

Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

Yunta¹

2014

AJMO

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Protonation states are sometimes crucial for free energy calculations to predict binding ability of molecules to receptors, a main subject for drug design. This mini-review seeks to identify the importance of knowing the influence of pH in such studies to better achieve correct predictions for drug candidates. Protonation states, for both proteins and drugs, need to be considered in docking studies although they have been usually neglected.

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Tautomerism in chemical information management systems

Cited by 45 publications

References 25 publications

Chemical databases: curation or integration by user-defined equivalence?

Chemical databases: curation or integration by user-defined equivalence?

A Branch‐and‐Bound Approach for Tautomer Enumeration

Some Critical Aspects of Molecular Interactions Between Drugs and Receptors

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