ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models
Brinda Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin Webb, Augustin Žídek, Wei Zheng, Ezra Peisach, Dennis W. Piehl, Ivan Anischanka, Ian Sillitoe, James Tolchard, Mihály Váradi, David Baker, Christine Orengo, Yang Zhang, Jeffrey C. Hoch, Genji Kurisu, Ardan Patwardhan, Sameer Velankar, S.K. Burley, Andrej Săli, Torsten Schwede, Helen M. Berman, John Westbrook
Abstract
ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.