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DeepRank · Sep 13, 2023 · 945f835 · 945f835
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 # Summary
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+![DeepRank2 framework overview. 3D coordinates of protein structures are extracted from PDB files and converted into graphs and grids, using either an atomic or a residual level, depending on the user’s requirements. The data are enriched with geometrical and physicochemical information and are stored into HDF5 files, and can then be used in the pre-implemented DL pipeline for training PyTorch networks and computing predictions.\label{fig:flowchart}](deeprank2.png)
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 # State of the field
 
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 This project is expected to have an impact across the all of structural bioinformatics, enabling advancements that rely on molecular complex analysis, such as structural biology, protein engineering, and rational drug design. The target community includes researchers working with molecular complexes data, such as computational biologists, immunologists, and structural bioinformatics scientists. The existing features, as well as the sustainable package formatting and its modular design make DeepRank2 an excellent framework to build upon. Taken together, DeepRank2 provides all the requirements to become the all-purpose DL tool that is currently lacking in the field of biomolecular interactions.
 
-![DeepRank2 framework overview. 3D coordinates of protein structures are extracted from PDB files and converted into graphs and grids, using either an atomic or a residual level, depending on the user’s requirements. The data are enriched with geometrical and physicochemical information and are stored into HDF5 files, and can then be used in the pre-implemented DL pipeline for training PyTorch networks and computing predictions.\label{fig:flowchart}](deeprank2.png)
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 # Acknowledgements
 
 This work was supported by the [Netherlands eScience Center](https://www.esciencecenter.nl/) under grant number NLESC.OEC.2021.008, and [SURF](https://www.surf.nl/en) infrastructure, and was developed in collaboration with the [Department of Medical BioSciences](https://www.radboudumc.nl/en/research/departments/medical-biosciences) at RadboudUMC.