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

This US RCSB Protein Data Bank (RCSB PDB) - UK Protein Data Bank in Europe (PDBe) collaborative project will significantly redesign existing open-source Molstar molecular graphics infrastructure to develop an extensible, one-stop-shop for visualization and interrogation of open-access three-dimensional (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. Molstar works entirely with the users internet browser (e.g., Chrome, Firefox, Safari).

It consists of an easy-to-use graphical interface with no user login or software product download, update, or registration required. The redesigned Molstar system will be FAIR (Findability, Accessibility, Interoperability, and Reusability) and FACT (Fairness, Accuracy, Confidentiality, Transparency) Principles compliant. It will support efficient data delivery and visualization and study of 3D structure data together with structural, biological, and functional annotations across length scales ranging from individual atoms to whole cells.

Researchers, educators, and students accessing the new system will be able to combine, visualize, and evaluate structure data and related biological, medical, and chemical information from multiple open-access data resources. It will also support analyses of 3D structures of biomolecules their respective in organellar or cellular contexts Users of the redesigned Molstar infrastructure will be able to study macromolecular machines (e.g., prokaryotic RNA Polymerase-Ribosome Super Complex; eukaryotic Nuclear Pore Complex) in 3D in situ combined with biological and functional information integrated from a diverse array of open-access biodata resources operating in the Americas, Europe, Oceania, and Asia.

This project will address significant challenges resulting from the growing corpus of 3D structure data stored in disparate open-access primary data resource. These include the need for integration and interoperation of these data with related biological and functional annotations from knowledgebases; the need for a standard data representation for display of 3D structure data across length scales; 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; the need to combine atomic level/multiscale structures with lower resolution information from cryo- electron tomography and super-resolution microscopy; and the need for efficient data packaging, compression, and delivery for users with diverse levels of internet connectivity.

The project will overcome current limitations in data management, interoperability, and visualization that make it difficult, sometimes impossible, for molecular, cellular, and organismal biologists to fully utilize the world’s open-access 3D biostructure data. The software products of the project will be freely accessible at https://www.molstar.org.

Utilization of the Molstar software will be exemplified within the web portals of RCSB PDB (https://www.rcsb.org) and PDBe (https://www.pdbe.org), which are available to all users at no charge and with no limitations on data usage under the most permissive Creative Commons CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0/).

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.