Streamlining Drug Discovery workflows with KNIME: Leveraging Open-Source Tools for Computational Drug Design

Author: Maryam Salehi

Editors: Andrew Whitehouse, Melchor Sanchez Martinez, Natalja Kurbatova, Euan Dean

Summary:

The Konstanz Information Minor (KNIME) is an open-source data pipelining and analytics platform which enables users to create (semi)automated workflows for data processing, transformation, analysis, and visualization. Additionally, it facilitates the generation and deployment of mathematical models. Therefore, it can be extremely useful if provided with the right plug-in. Zifo has expertise in creating well-structured and complex workflows. If you want to know how you can benefit from KNIME, please get in touch with us at [email protected]

Introduction:

Computational tools play a crucial role in computer-aided drug design (CADD), where they are employed to process and rationalize large and diverse datasets, including chemicals and proteins. The availability of open-access life science repositories like CHEMBL, PubChem, UniProt, and DrugBank offers a competitive advantage for data-driven drug discovery compared to non-integrative approaches. Moreover, most of these databases supply programmatic access to their stored data through application programming interfaces (APIs). Consequently, open-access resources have gained significant attention, especially for generating complex workflows, as they facilitate the development of modular, reproducible, and reusable research methodologies.

Applications:

KNIME is a versatile platform that empowers users with an open-source data analysis, integration, and reporting solution. Through KNIME, users can construct data workflows, execute specific analysis steps, evaluate results and models, and have interactive visualization through a graphical user interface. Coding is unnecessary as the workflows are built by connecting pre-implemented code units (referred to as nodes) with thoroughly tested and standardized functionalities. However, these nodes can be further customized with individual settings for specific requirements, and new nodes can even be created from scratch if needed.

KNIME is widely recognized as a common data science workflow manager, offering numerous open-source modules for CADD. Its application spans from simple in-house tasks like preparing compound libraries to more intricate workflow applications incorporating chemical, pharmaceutical, and structural data. The KNIME community is very active and, over the past few years, has released many CADD-related nodes like RDKIT or Chemistry Development Kit (CDK). The most popular tools in CADD, offered as standalone software or libraries for coding languages, are now accessible as KNIME nodes.

Benefits:

Semiautomated drug discovery pipelines leverage the advantage of computational workflows, particularly through the utilization of open-source tools like KNIME, in combination with the availability of large-scale open-source tools that can be programmatically accessed. These pipelines facilitate easier access to data resources, thereby reducing barriers to effective data utilization for non-data scientists. Additionally, they expedite the process from data collection to the discovery of hidden relationships within the data. Furthermore, such workflows are highly reproducible and can be adapted to meet the specific needs of individual projects.

Discover the potential of KNIME with our specialized support tailored to your needs. Our skilled team offers comprehensive assistance, empowering you to leverage its advanced functionalities, streamline workflows and drive innovation to achieve your objectives. For more information, please do not hesitate to contact us at [email protected].