ModelCIF
ModelCIF provides an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) for representing predicted three-dimensional (3D) macromolecular models (computed structure models, CSMs) to support deposition, archiving, and FAIR (Findable, Accessible, Interoperable, and Reusable) dissemination of computational structural data.
Key Features:
- PDBx/mmCIF extension: Extends the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) schema to accommodate attributes specific to computational models.
- CSM representation: Describes macromolecular structures derived exclusively from computational methods, including predicted three-dimensional (3D) models and computed structure models (CSMs).
- Metadata capture: Records detailed metadata and model-specific attributes required for deposition, archiving, and public dissemination of computational models.
- Semantic richness and FAIR support: Encodes semantically rich information intended to enable Findable, Accessible, Interoperable, and Reusable (FAIR) computational structural data.
- Integration with structural resources: Enables integration of computationally derived models into existing databases and tools used by structural biologists.
- Governance: Maintained under the Worldwide Protein Data Bank (wwPDB) partnership with contributions from the wwPDB ModelCIF Working Group.
- Community tooling and libraries: Supported by community tools and software libraries for maintaining and extending the data standard.
Scientific Applications:
- Deposition and archiving: Standardizes deposition and archival representation of predicted 3D macromolecular models and CSMs.
- Public dissemination: Facilitates public sharing and dissemination of computational structural models.
- Interoperability and data sharing: Promotes interoperability and standardized data exchange among structural biology databases and analysis tools.
- Reuse of computational models: Enables reuse and comparative analysis of computational models by providing consistent metadata and model descriptors.
Methodology:
Extends the PDBx/mmCIF schema to represent computationally derived macromolecular models and associated metadata.
Topics
Details
- License:
- CC0-1.0
- Cost:
- Free of charge
- Tool Type:
- command-line tool
- Operating Systems:
- Mac, Linux, Windows
- Programming Languages:
- Shell, Python
- Added:
- 4/27/2023
- Last Updated:
- 4/27/2023
Operations
Publications
Vallat B, Tauriello G, Bienert S, Haas J, Webb BM, Žídek A, Zheng W, Peisach E, Piehl DW, Anischanka I, Sillitoe I, Tolchard J, Varadi M, Baker D, Orengo C, Zhang Y, Hoch JC, Kurisu G, Patwardhan A, Velankar S, Burley SK, Sali A, Schwede T, Berman HM, Westbrook JD. ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models. Journal of Molecular Biology. 2023;435(14):168021. doi:10.1016/j.jmb.2023.168021. PMID:36828268. PMCID:PMC10293049.