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Dockground: The Resource Expands to Protein-RNA Interactome
Keeley W Collins1, Matthew M Copeland1, Petras J Kundrotas1
1Computational Biology Program, The University of Kansas, Lawrence, KS 66045, United States.
Abstract:
RNA is a master regulator of cellular processes and will bind to many different proteins throughout its life cycle. Dysregulation of RNA and RNA-binding proteins can lead to various diseases, including cancer. To better understand molecular mechanisms of the cellular processes, it is important to characterize protein-RNA interactions at the structural level. There is a lack of experimental structures available for protein-RNA complexes due to the RNA inherent flexibility, which complicates the experimental structure determination. The scarcity of structures can be made up for with computational modeling. Dockground is a resource for development and benchmarking of structure-based modeling of protein interactions. It contains datasets focusing on different aspects of protein recognition. The foundation of all the datasets is the database of experimentally determined protein complexes, which previously contained only protein-protein assemblies. To further expand the utility of the Dockground resource, we extended the database to protein-RNA interactions. The new functionalities are available on the Dockground website at https://dockground.compbio.ku.edu/. The database can be searched using a number of criteria, including removal of redundancies at various sequence and structure similarity thresholds. The database updates with new structures from the Protein Data Bank on a weekly basis.
Insights
Computational modeling aids in understanding protein-RNA interactions, crucial for cellular processes and disease research. The Dockground database now includes protein-RNA complexes to support this research.
Area of Science:
- Structural Biology
- Computational Biology
- Molecular Biology
Background:
- RNA regulates cellular processes and binds proteins; dysregulation is linked to diseases like cancer.
- Characterizing protein-RNA interactions structurally is vital for understanding molecular mechanisms.
- RNA's flexibility complicates experimental structure determination, leading to a scarcity of available data.
Purpose of the Study:
- To expand the Dockground resource for computational modeling of protein-RNA interactions.
- To provide a comprehensive database of experimentally determined protein-RNA complexes.
- To facilitate the development and benchmarking of structure-based modeling techniques for protein-RNA systems.
Main Methods:
- Extended the Dockground database to include protein-RNA interactions.
- Integrated new functionalities on the Dockground website (https://dockground.compbio.ku.edu/).
- Enabled searching by various criteria, including redundancy removal at different similarity thresholds.
- Implemented weekly updates with new structures from the Protein Data Bank.
Main Results:
- The Dockground resource now contains a dedicated dataset for protein-RNA interactions.
- The updated website offers enhanced search and data management capabilities.
- The database is regularly updated, ensuring access to the latest structural information.
- Facilitated computational modeling efforts by providing a valuable resource.
Conclusions:
- The expanded Dockground database significantly enhances the study of protein-RNA interactions.
- This resource supports the development of computational methods for structure-based modeling.
- It aids researchers in understanding the structural basis of cellular processes and diseases involving RNA-binding proteins.
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