20-BBSRC/NSF-BIO: From atoms to molecules to cells - Multi-scale tools and infrastructure for visualization of annotated 3D structure data

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This project will significantly redesign existing open-source Molstar molecular graphics infrastructure (molstar.org) to develop an extensible, one-stop-shop for web-native visualization and interrogation of open-access 3D structure data integrated from the Protein Data Bank (PDB), NextGen PDB, PDB-Dev, Electron Microscopy Data Bank, Electron Microscopy Image Archive, and BioImage Archive. The redesigned system will support efficient data delivery and web-native visualization and interrogation of 3D multiscale structure data together with structural, biological, and functional annotations across length scales ranging from individual atoms to whole cells. To the best of our knowledge, no similar software tools are currently available. Researchers, educators, and students accessing the new system will be able to combine, visualize, and interrogate structural information and related annotations from multiple open-access data resources and analyze 3D multiscale structures their respective in organellar or cellular contexts.
The joint project addresses significant challenges resulting from:
(i) the growing corpus of 3D structure data stored in disparate open-access primary data resources
(ii) the need for integration and interoperation of these data with related biological and functional annotations from knowledgebases
(iii) the need for a standard data representation for display of 3D structure data across length scales
(iv) the need to examine multiple 3D structures of biological macromolecules in groups of related structures coming from cutting-edge techniques such as serial femtosecond X-ray crystallography and cryo-electron microscopy
(v) the need to combine atomic
level/multiscale structures with lower resolution information from cryo-electron tomography and superresolution microscopy
(vi) the need for efficient data packaging, compression, and delivery for users with diverse levels of internet connectivity.