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Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)

  • The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day.

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Metadaten
Author:Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
DOI:https://doi.org/https://doi.org/10.1186/s13321-022-00656-x
ISSN:1758-2946
Parent Title (English):Journal of Cheminformatics
Publisher:BioMed Central
Place of publication:London
Document Type:Article
Language:English
Date of Publication (online):2022/11/10
Date of first Publication:2022/11/10
Publishing Institution:Westfälische Hochschule Gelsenkirchen Bocholt Recklinghausen
Release Date:2023/03/14
Tag:CDK; Chemical space; Cheminformatics; Chemistry Development Kit; Clustering; Fragmentation; Natural products; Scaffold; Scaffold network; Scaffold tree
Volume:2022
Issue:14:79
Pagenumber:25
Departments / faculties:Institute / Institut für biologische und chemische Informatik
Licence (German):License LogoEs gilt das Urheberrechtsgesetz

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