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J Biomol NMR. 2019 Jul;73(6-7):385-398. doi: 10.1007/s10858-019-00264-2. Epub 2019 Jul 5.

Archiving and disseminating integrative structure models.

Author information

1
Institute for Quantitative Biomedicine, Piscataway, USA.
2
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA, 94143, USA.
3
RCSB Protein Data Bank, Piscataway, USA.
4
RCSB Protein Data Bank, Piscataway, USA. sali@salilab.org.
5
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA, 94143, USA. sali@salilab.org.
6
Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, 94143, USA. sali@salilab.org.
7
Lead Contacts, San Francisco, USA. sali@salilab.org.
8
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA. berman@rcsb.rutgers.edu.
9
Lead Contacts, Piscataway, USA. berman@rcsb.rutgers.edu.

Abstract

Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format.

KEYWORDS:

Deposition; Hybrid modeling; Integrative modeling; Model validation; PDB; mmCIF dictionary

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