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The C++?programming language in cheminformatics and computational chemistry.

ABSTRACT: This paper describes salient features of the C++ programming language and its programming ecosystem, with emphasis on how the language affects scientific software development. Brief history of C++ and its predecessor the C language is provided. Most important aspects of the language that define models of programming are described in greater detail and illustrated with code examples. Special attention is paid to the interoperability between C++ and other high-level languages commonly used in cheminformatics, machine learning, data processing and statistical computing.

SUBMITTER: Rassokhin D

PROVIDER: S-EPMC7006409 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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The C++ programming language in cheminformatics and computational chemistry.

Rassokhin Dmitrii D

Journal of cheminformatics 20200207 1

This paper describes salient features of the C++ programming language and its programming ecosystem, with emphasis on how the language affects scientific software development. Brief history of C++ and its predecessor the C language is provided. Most important aspects of the language that define models of programming are described in greater detail and illustrated with code examples. Special attention is paid to the interoperability between C++ and other high-level languages commonly used in chem ...[more]

PMID: 33431041

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Project description:BackgroundThe dynamic and differential regulation and expression of genes is majorly governed by the complex interactions of a subset of biomolecules in the cell operating at multiple levels starting from genome organisation to protein post-translational regulation. The regulatory layer contributed by the epigenetic layer has been one of the favourite areas of interest recently. This layer of regulation as we know today largely comprises of DNA modifications, histone modifications and noncoding RNA regulation and the interplay between each of these major components. Epigenetic regulation has been recently shown to be central to development of a number of disease processes. The availability of datasets of high-throughput screens for molecules for biological properties offer a new opportunity to develop computational methodologies which would enable in-silico screening of large molecular libraries.MethodsIn the present study, we have used data from high throughput screens for the inhibitors of epigenetic modifiers. Computational predictive models were constructed based on the molecular descriptors. Machine learning algorithms for supervised training, Naive Bayes and Random Forest, were used to generate predictive models for the small molecule inhibitors of histone methyl-transferases and demethylases. Random forest, with the accuracy of 80%, was identified as the most accurate classifier. Further we complemented the study with substructure search approach filtering out the probable pharmacophores from the active molecules leading to drug molecules.ResultsWe show that effective use of appropriate computational algorithms could be used to learn molecular and structural correlates of biological activities of small molecules. The computational models developed could be potentially used to screen and identify potential new biological activities of molecules from large molecular libraries and prioritise them for in-depth biological assays. To the best of our knowledge, this is the first and most comprehensive computational analysis towards understanding activities of small molecules inhibitors of epigenetic modifiers.

Dataset Information

The C++?programming language in cheminformatics and computational chemistry.

Publications

The C++ programming language in cheminformatics and computational chemistry.

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