PIKAChU: a Python-based informatics kit for analysing chemical units

As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate,...

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Veröffentlicht in:Journal of cheminformatics Jg. 14; H. 1; S. 34 - 17
Hauptverfasser: Terlouw, Barbara R., Vromans, Sophie P. J. M., Medema, Marnix H.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Cham Springer International Publishing 07.06.2022
BioMed Central Ltd
Springer Nature B.V
BMC
Schlagworte:
Analysis
Aromaticity
Bioinformatics
Cheminformatics kit
Chemistry
Chemistry and Materials Science
Chirality
Computational Biology/Bioinformatics
Computer Applications in Chemistry
Computer programs
Documentation and Information in Chemistry
Electron orbitals
Fingerprinting
Graphs
Hybridization
In silico chemistry
Informatics
Molecular fingerprinting
Programming languages
Python
Reaction mechanisms
Software
Structure visualisation
Theoretical and Computational Chemistry
Toolkits
Visualization
Visualization (Computers)
Web applications
Cheminformatics kit
Molecular fingerprinting
Structure visualisation
In silico chemistry
Python
ISSN:1758-2946, 1758-2946
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Zusammenfassung:As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate, or not written in Python, the programming language of choice for bioinformaticians. Here, we introduce PIKAChU (Python-based Informatics Kit for Analysing CHemical Units): a cheminformatics toolbox with few dependencies implemented in Python. PIKAChU builds comprehensive molecular graphs from SMILES strings, which allow for easy downstream analysis and visualisation of molecules. While the molecular graphs PIKAChU generates are extensive, storing and inferring information on aromaticity, chirality, charge, hybridisation and electron orbitals, PIKAChU limits itself to applications that will be sufficient for most casual users and downstream Python-based tools and databases, such as Morgan fingerprinting, similarity scoring, substructure matching and customisable visualisation. In addition, it comes with a set of functions that assists in the easy implementation of reaction mechanisms. Its minimalistic design makes PIKAChU straightforward to use and install, in stark contrast to many existing toolkits, which are more difficult to navigate and come with a plethora of dependencies that may cause compatibility issues with downstream tools. As such, PIKAChU provides an alternative for researchers for whom basic cheminformatic processing suffices, and can be easily integrated into downstream bioinformatics and cheminformatics tools. PIKAChU is available at https://github.com/BTheDragonMaster/pikachu . Graphical Abstract
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ISSN:1758-2946
1758-2946
DOI:10.1186/s13321-022-00616-5