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. 2019 Jan 1:2019:baz101.
doi: 10.1093/database/baz101.

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

Leo William Norval  1   2 , Stefan Daniel Krämer  1   3 , Mingjie Gao  2 , Tobias Herz  1   3 , Jianyu Li  2 , Christin Rath  1   3   4   5 , Johannes Wöhrle  1   6 , Stefan Günther  2 , Günter Roth  1   3   4   5
Affiliations

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

Leo William Norval et al. Database (Oxford). .

Abstract

The kinetics of featured interactions (KOFFI) database is a novel tool and resource for binding kinetics data from biomolecular interactions. While binding kinetics data are abundant in literature, finding valuable information is a laborious task. We used text extraction methods to store binding rates (association, dissociation) as well as corresponding meta-information (e.g. methods, devices) in a novel database. To date, over 270 articles were manually curated and binding data on over 1705 interactions was collected and stored in the (KOFFI) database. Moreover, the KOFFI database application programming interface was implemented in Anabel (open-source software for the analysis of binding interactions), enabling users to directly compare their own binding data analyses with related experiments described in the database.

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Figures

Figure 1
Figure 1
(A) Annotated interactions by year and method. Depicted are the yearly interaction counts for major methods in the order of appearance. (B) Overall interactions annotated by method (rounded).
Figure 2
Figure 2
Normalized distribution of KD values by method. Shown are the frequencies of interactions with a KD in a specific range for the major methods SPR and BLI. Other methods are summarized.
Figure 3
Figure 3
Data quality. All annotators were encouraged to rate the underlying data of the binding events using four different questions (A–C). Hereby, the graphs B and C are relative to data classified with ‘Yes’ in graph A. Graph D shows the relative values to the data classified with ‘Yes’ in graph C.
Figure 4
Figure 4
kdiss/kass plot produced using Anabel’s ‘KOFFI database analysis’ module. The evaluated real-life dataset is illustrated as colored dots, whereas the database search results are shown as colored labels with black rhombuses. KD lines are drawn as gray lines with their corresponding values at the edges of the graph.
See this image and copyright information in PMC

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