ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK)

Fritsch, Sebastian; Neumann, Stefan; Schaub, Jonas; Steinbeck, Christoph; Zielesny, Achim

doi:10.1186/s13321-019-0361-8

Cited by 15 publications

(11 citation statements)

References 6 publications

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“…The actual extraction of FGs has been done by an in-house toolkit written in Java . In the meantime, open source versions of this protocol have been made available in Python and also in Java; therefore the whole computational procedure can now be performed using open source software.…”

Section: Computational Methodologymentioning

confidence: 99%

A Systematic Cheminformatics Analysis of Functional Groups Occurring in Natural Products

2019

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The two most striking features that discriminate natural products from synthetic molecules are their characteristic scaffolds and unique functional groups (FGs). In this study we systematically investigate the distribution of FGs in natural products from a cheminformatics perspective by comparing FG frequencies in natural products with those found in average synthetic molecules. We thereby aim for the identification of FGs that are characteristic for molecules produced by living organisms. In our analysis we also include information about the natural origins of the structures investigated, allowing us to link the occurrence of specific FGs to the individual producing species. Our findings have the potential for being applied in a medicinal chemistry context concerning the synthesis of natural product-like libraries and natural product-inspired fragment collections. The results may be used also to support compound derivatization strategies and the design of “non-natural” natural products.

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Section: Computational Methodologymentioning

confidence: 99%

A Systematic Cheminformatics Analysis of Functional Groups Occurring in Natural Products

2019

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“…ClassyFire provides a hierarchical chemical classification of chemical compounds and enables grouping NPs by their chemical class. Additionally, frameworks facilitating NPs analyses for their chemical and therapeutic properties are computed for NPs, such as Murcko frameworks [15], Ertl Functional Groups [16] and deepSMILES [17]. DeepSMILES is an adaptation of SMILES for use in deep machine learning of chemical structures.…”

Section: Most Resent Publication or Resource Urlmentioning

confidence: 99%

COCONUT online: Collection of Open Natural Products database

et al. 2021

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Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net.

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“…Although the actual extraction of FGs was performed by an inhouse toolkit written in Java, in the interim, two open-source versions of this algorithm have been made available, namely in Python 12 and also in Java, 13 and therefore, the complete computational procedure described here can be performed using the open-source software at will.…”

Section: T H Imentioning

confidence: 99%

The Most Common Functional Groups in Bioactive Molecules and How Their Popularity Has Evolved over Time

Ertl

Altmann

McKenna³

2020

J. Med. Chem.

233

156

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The concept of functional groups (FGs), sets of connected atoms that can determine the intrinsic reactivity of the parent molecule and in part are responsible for the overall properties of the molecule, form a foundation within modern medicinal chemistry. In this Article, we analyze the occurrence of various FGs in molecules described in the medicinal chemistry literature over the last 40 years and show how their development and utilization over time has varied. The popularity of various FGs has not evolved randomly, but instead, clear patterns of use are evident. Various factors influencing these patterns, including the introduction of new synthetic methods, novel techniques, and strategies applied in drug discovery and the better knowledge of molecular properties affecting the success of candidate development, are discussed.

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ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK)

Cited by 15 publications

References 6 publications

A Systematic Cheminformatics Analysis of Functional Groups Occurring in Natural Products

A Systematic Cheminformatics Analysis of Functional Groups Occurring in Natural Products

COCONUT online: Collection of Open Natural Products database

The Most Common Functional Groups in Bioactive Molecules and How Their Popularity Has Evolved over Time

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