KOFFI and Anabel 2.0-a new binding kinetics database and its integration in an open-source binding analysis software

Area of Science:

• Biochemistry
• Molecular Biology
• Bioinformatics

Background:

• Binding kinetics data are crucial for understanding biomolecular interactions.
• Existing literature contains abundant binding kinetics data, but accessing it is challenging and time-consuming.
• A centralized, searchable resource for this data is needed.

Purpose of the Study:

• To develop a novel database, the Kinetics of Featured Interactions (KOFFI) database, for storing and accessing biomolecular binding kinetics data.
• To facilitate the retrieval of binding rates (association and dissociation) and associated metadata.
• To integrate the database with analysis software for direct comparison of experimental data.

Main Methods:

• Manual curation of over 270 scientific articles.
• Application of text extraction methods to identify and record binding kinetics data.
• Development of a database to store over 1705 unique biomolecular interactions.
• Implementation of an application programming interface (API) for the KOFFI database.

Main Results:

• The KOFFI database successfully compiles binding kinetics data from a significant number of publications.
• Over 1705 biomolecular interactions with associated kinetic data have been stored.
• The KOFFI database API is integrated into Anabel, an open-source analysis software.

Conclusions:

• The KOFFI database provides a valuable, centralized resource for biomolecular binding kinetics.
• Researchers can efficiently access and compare binding data, accelerating research.
• The integration with Anabel enhances the utility of the KOFFI database for experimental analysis.