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

Jonas Schaub; Julian Zander; Achim Zielesny; Christoph Steinbeck

doi:10.1186/s13321-022-00656-x

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

J Cheminform. 2022 Nov 10;14(1):79. doi: 10.1186/s13321-022-00656-x.

Authors

Jonas Schaub¹, Julian Zander², Achim Zielesny², Christoph Steinbeck³

Affiliations

¹ Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743, Jena, Germany.
² Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, 45665, Recklinghausen, Germany.
³ Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessing Strasse 8, 07743, Jena, Germany. christoph.steinbeck@uni-jena.de.

Abstract

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.

Keywords: CDK; Chemical space; Cheminformatics; Chemistry Development Kit; Clustering; Fragmentation; Natural products; Scaffold; Scaffold network; Scaffold tree.