Stefan Kohlbacher, Gökhan Ibis, Christian Permann, Sharon Bryant, Thierry Langer, Thomas Seidel
{"title":"A new set of KNIME nodes implementing the QPhAR algorithm.","authors":"Stefan Kohlbacher, Gökhan Ibis, Christian Permann, Sharon Bryant, Thierry Langer, Thomas Seidel","doi":"10.1002/minf.202200245","DOIUrl":null,"url":null,"abstract":"<p><p>Dissemination of novel research methods, especially in the form of chemoinformatics software, depends heavily on their ease of applicability for non-expert users with only a little or no programming skills and knowledge in computer science. Visual programming has become widely popular over the last few years, also enabling researchers without in-depth programming skills to develop tailored data processing pipelines using elements from a repository of predefined standard procedures. In this work, we present the development of a set of nodes for the KNIME platform implementing the QPhAR algorithm. We show how the developed KNIME nodes can be included in a typical workflow for biological activity prediction. Furthermore, we present best-practice guidelines that should be followed to obtain high-quality QPhAR models. Finally, we show a typical workflow to train and optimise a QPhAR model in KNIME for a set of given input compounds, applying the discussed best practices.</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":null,"pages":null},"PeriodicalIF":2.8000,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Informatics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1002/minf.202200245","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0
Abstract
Dissemination of novel research methods, especially in the form of chemoinformatics software, depends heavily on their ease of applicability for non-expert users with only a little or no programming skills and knowledge in computer science. Visual programming has become widely popular over the last few years, also enabling researchers without in-depth programming skills to develop tailored data processing pipelines using elements from a repository of predefined standard procedures. In this work, we present the development of a set of nodes for the KNIME platform implementing the QPhAR algorithm. We show how the developed KNIME nodes can be included in a typical workflow for biological activity prediction. Furthermore, we present best-practice guidelines that should be followed to obtain high-quality QPhAR models. Finally, we show a typical workflow to train and optimise a QPhAR model in KNIME for a set of given input compounds, applying the discussed best practices.
期刊介绍：
Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010.
Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation.
The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
