ArticleBMC bioinformatics2013
KNIME-CDK: Workflow-driven cheminformatics.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
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- Zombie cheminformatics: extraction and conversion of Wiswesser Line Notation (WLN) from chemical documents.Journal of cheminformatics · 2024Article
- Current state of data stewardship tools in life science.Frontiers in big data · 2024Review
- An Automated, Open-Source Workflow for the Generation of (3D) Fragment Libraries.ACS medicinal chemistry letters · 2023Article
- Predictive Models for Human Cytochrome P450 3A7 Selective Inhibitors and Substrates.Journal of chemical information and modeling · 2023Article
- SuperNatural 3.0-a database of natural products and natural product-based derivatives.Nucleic acids research · 2023Article
- Consensus Virtual Screening Protocol Towards the Identification of Small Molecules Interacting with the Colchicine Binding Site of the Tubulin-microtubule System.Molecular informatics · 2023Article
- Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases.ACS omega · 2022Article
- PIKAChU: a Python-based informatics kit for analysing chemical units.Journal of cheminformatics · 2022Article
- Efficient automatic 3D segmentation of cell nuclei for high-content screening.BMC bioinformatics · 2022Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
6 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
backgroundCheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process.
resultsKNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest.
conclusionsKNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.