ModelCIF Extension for Computed Structure Models
ModelCIF, an extension of PDBx/mmCIF for computed structure models, is now available. The PDBx/mmCIF data standard underpins the Protein Data Bank (PDB) Core Archive, which is jointly managed by the worldwide Protein Data Bank (wwPDB) consortium. A software library called python-modelcif has been developed to support ModelCIF and enables reading and writing mmCIF files compliant with ModelCIF.
ModelCIF serves as the data standard for representing structural models of macromolecules obtained using computational methods. These computed structure models may be derived from existing structure templates using homology or comparative modeling or can be obtained from ab initio modeling methods. ModelCIF data standard is being adopted by computational biologists as well as major repositories of computed structure models, including ModelArchive, MODBASE, and AlphaFoldDB Protein Structure Database repositories for computed structure models. Partial support for ModelCIF is also available in SWISS-MODEL projects and will soon be added to the SWISS-MODEL Repository.
ModelCIF is developed and maintained by the wwPDB ModelCIF Working Group (WG), consisting of representatives from the wwPDB and the computational structural biology community. The WG is focused on developing common data standards and software tools for archiving and visualization of computed structure models. The WG promotes adoption of ModelCIF within the computational modeling community, and is also involved in developing software tools that support ModelCIF. Research teams making computed structure models available from their own web portals are strongly encouraged to do so using the ModelCIF data standard and integrate them into the 3D-Beacons network. Structural biologists are strongly encouraged to deposit computed structure models to the ModelArchive to ensure long-term preservation and public access. Guidelines on how to deposit computed structure models together with relevant metadata are also available on ELIXIR's RDMkit page for structural bioinformatics.