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Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures
- Source :
- Structure/Folding and Design, 27(12), 1745, Berman, H M, Adams, P D, Bonvin, A A, Burley, S K, Carragher, B, Chiu, W, DiMaio, F, Ferrin, T E, Gabanyi, M J, Goddard, T D, Griffin, P R, Haas, J, Hanke, C A, Hoch, J C, Hummer, G, Kurisu, G, Lawson, C L, Leitner, A, Markley, J L, Meiler, J, Montelione, G T, Phillips, G N, Prisner, T, Rappsilber, J, Schriemer, D C, Schwede, T, Seidel, C A M, Strutzenberg, T S, Svergun, D I, Tajkhorshid, E, Trewhella, J, Vallat, B, Velankar, S, Vuister, G W, Webb, B, Westbrook, J D, White, K L & Sali, A 2019, ' Federating structural models and data : Outcomes from a workshop on archiving integrative structures ', Structure, vol. 27, no. 12, pp. 1745-1759 . https://doi.org/10.1016/j.str.2019.11.002, Structure, Structure (London, England : 1993), vol 27, iss 12
- Publication Year :
- 2019
-
Abstract
- Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards , building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here. Introduction When the Protein Data Bank (PDB) (Protein Data Bank, 1971) was first established in 1971, X-ray crystallography was the only method for determining three-dimensional structures of biological macromolecules at sufficient resolution to build atomic models. A decade later, structures of biomolecules in solution could also be determined by nuclear magnetic resonance (NMR) spectroscopy (Williamson et al., 1985). Recently, three-dimensional cryoelectron microscopy (3DEM) (Henderson et al., 1990) began to achieve unprecedented near-atomic resolution for large complex assemblies. Increasingly, investigators are also modeling structures based on data from more than one method (Rout and Sali, 2019). These integrative/hybrid approaches to structure determination consist of collecting information about a system using multiple experimental and computational methods, followed by integrative/hybrid modeling that converts this information into integrative/hybrid structure models. For succinctness, we will use the term integra-tive hereafter to refer to integrative/hybrid approaches, modeling, and models.
- Subjects :
- Magnetic Resonance Spectroscopy
Protein Conformation
Computer science
Biophysics
Article
Databases
03 medical and health sciences
Models
Structural Biology
Information and Computing Sciences
Taverne
Molecular Biology
030304 developmental biology
0303 health sciences
Crystallography
Extramural
Protein
030302 biochemistry & molecular biology
Proteins
Computational Biology
Molecular
Biological Sciences
Data science
Data exchange
Chemical Sciences
X-Ray
Experimental methods
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Structure/Folding and Design, 27(12), 1745, Berman, H M, Adams, P D, Bonvin, A A, Burley, S K, Carragher, B, Chiu, W, DiMaio, F, Ferrin, T E, Gabanyi, M J, Goddard, T D, Griffin, P R, Haas, J, Hanke, C A, Hoch, J C, Hummer, G, Kurisu, G, Lawson, C L, Leitner, A, Markley, J L, Meiler, J, Montelione, G T, Phillips, G N, Prisner, T, Rappsilber, J, Schriemer, D C, Schwede, T, Seidel, C A M, Strutzenberg, T S, Svergun, D I, Tajkhorshid, E, Trewhella, J, Vallat, B, Velankar, S, Vuister, G W, Webb, B, Westbrook, J D, White, K L & Sali, A 2019, ' Federating structural models and data : Outcomes from a workshop on archiving integrative structures ', Structure, vol. 27, no. 12, pp. 1745-1759 . https://doi.org/10.1016/j.str.2019.11.002, Structure, Structure (London, England : 1993), vol 27, iss 12
- Accession number :
- edsair.doi.dedup.....a9744ce02a34f96adf3126d6435a8f03