VLVS: A Knime Based Virtual Library Generation and Screening Workflow
Ismail Hakki Akgün
*
Department of Bioengineering, Faculty of Engineering, Ege University, 35100, Bornova, İzmir, Türkiye.
*Author to whom correspondence should be addressed.
Abstract
Objective: Tocreate an easy-to-use structure-based screening workflow using KNIME and open source software to prepare and screen virtual libraries in order to discover novel bioactive or drug molecules.
Materials and Methods: In the preparation of the workflow we mentioned in the article KNIME version 4, AutoDock Vina, Pymol were used. KNIME plugins used in this study are RDKit KNIME Integration, ChemAxon/Infocom Marvin Extensions Feature, KNIME Python Integration, Lhasa Metabolism Feature, KNIME Ploty and KNIME JavaScript View. We have used Python3 and libraries in the python scripts through Anaconda installation.
Results: A workflow that can work with a single click after making required adjustments which uses docking as structure-based screening method was created and tested.
Conclusion: With the workflow we have created, it will be possible for researchers especially those who are working in the field of computer-aided drug design/development to create personalized molecule libraries, perform virtual screening, reporting the results in a short time with the least effort.
Keywords: Bioactive molecule design, virtual screening, docking, virtual library, drug design, drug discovery.