A home for integrative structural models

A home for integrative structural models research highlights STRUCTURAL BIOLOGY PDB-Dev hosts integrative structural models of biomolecular assemblies solved by hybrid methods. he Protein Data Bank, or PDB, is others—to generate spatial restraints. These At the moment, preliminary validation an essential resource for archiving, spatial restraints provide key clues about the metrics are available in PDB-Dev, but Tvalidating and disseminating arrangement of assembly subunits and are further community input will be needed to biomolecular structure models to a broad applied in ‘integrative’ modeling pipelines develop such metrics for integrative models. community. Currently over 135,000 for structure determination. PDB-Dev currently contains nine structure models—determined by X-ray The PDB, however, does not have the integrative models and is open for new crystallography, nuclear magnetic resonance infrastructure to handle models produced submissions at https://pdb-dev.wwpdb. (NMR) spectroscopy and cryo-electron via hybrid methods. With the development org. The resource will surely have a positive microscopy (cryo-EM)—can be found of a prototype system, PDB-Dev, integrative impact and facilitate greater reproducibility in the PDB. models now have a home. and transparency in structural studies of Despite recent remarkable technological Integrative models pose several biological assemblies. advances for structure analysis, especially in challenges for archiving. Such models Allison Doerr the field of cryo-EM, there are many large, may contain multiple resolution scales or complex, dynamic biomolecular assemblies conformational states, or may be represented Published online: 31 May 2018 that just cannot be solved with a single as ensembles of structures. PDB-Dev https://doi.org/10.1038/s41592-018-0032-0 structure-determination technique. To solve was built on the existing data standard these challenging structures, researchers for the PDB, ensuring interoperability Research papers can apply ‘hybrid’ methods—including and extensibility. Besides the integrative Vallat, B. et al. Development of a prototype system lower-resolution approaches such as electron models themselves, PDB-Dev archives the for archiving integrative/hybrid structure models tomography, small-angle X-ray scattering, experimental spatial restraints, modeling of biological macromolecules. Structu rh ettps://doi. cross-linking–mass spectrometry and pipelines used and associated metadata. org/10.1016/j.str.2018.03.011 (2018). NEW! Open Design Upright Microscope Simple coarse height adjustment Built-in motorized focus In vivo and In vitro experimentation on one setup OCC or DIC transmitted light (LED) Epi-u fl orescent imaging Uses standard Olympus objectives BOB The Sutter BOB – designed to eliminate the conventional microscope frame – is a versatile, open-design upright microscope platform ideal for slice electrophysiology, widefield fluorescent imaging, two-photon imaging, photostimulation and new techniques just being developed! PHONE: 415.883.0128 | FA X: 415.883.0572 EMAIL: INFO@SUT TER.COM | W W W.SUT TER.COM Nature Methods | VOL 15 | JUNE 2018 | 403–409 | www.nature.com/naturemethods © 2018 Nature America Inc., part of Springer Nature. All rights reserved. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Nature Methods Springer Journals

A home for integrative structural models

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Publisher
Springer Journals
Copyright
Copyright © 2018 by The Author(s)
Subject
Life Sciences; Life Sciences, general; Biological Techniques; Biological Microscopy; Biomedical Engineering/Biotechnology; Bioinformatics; Proteomics
ISSN
1548-7091
eISSN
1548-7105
D.O.I.
10.1038/s41592-018-0032-0
Publisher site
See Article on Publisher Site

Abstract

research highlights STRUCTURAL BIOLOGY PDB-Dev hosts integrative structural models of biomolecular assemblies solved by hybrid methods. he Protein Data Bank, or PDB, is others—to generate spatial restraints. These At the moment, preliminary validation an essential resource for archiving, spatial restraints provide key clues about the metrics are available in PDB-Dev, but Tvalidating and disseminating arrangement of assembly subunits and are further community input will be needed to biomolecular structure models to a broad applied in ‘integrative’ modeling pipelines develop such metrics for integrative models. community. Currently over 135,000 for structure determination. PDB-Dev currently contains nine structure models—determined by X-ray The PDB, however, does not have the integrative models and is open for new crystallography, nuclear magnetic resonance infrastructure to handle models produced submissions at https://pdb-dev.wwpdb. (NMR) spectroscopy and cryo-electron via hybrid methods. With the development org. The resource will surely have a positive microscopy (cryo-EM)—can be found of a prototype system, PDB-Dev, integrative impact and facilitate greater reproducibility in the PDB. models now have a home. and transparency in structural studies of Despite recent remarkable technological Integrative models pose several biological assemblies. advances for structure analysis, especially in challenges for archiving. Such models Allison Doerr the field of cryo-EM, there are many large, may contain multiple resolution scales or complex, dynamic biomolecular assemblies conformational states, or may be represented Published online: 31 May 2018 that just cannot be solved with a single as ensembles of structures. PDB-Dev https://doi.org/10.1038/s41592-018-0032-0 structure-determination technique. To solve was built on the existing data standard these challenging structures, researchers for the PDB, ensuring interoperability Research papers can apply ‘hybrid’ methods—including and extensibility. Besides the integrative Vallat, B. et al. Development of a prototype system lower-resolution approaches such as electron models themselves, PDB-Dev archives the for archiving integrative/hybrid structure models tomography, small-angle X-ray scattering, experimental spatial restraints, modeling of biological macromolecules. Structu rh ettps://doi. cross-linking–mass spectrometry and pipelines used and associated metadata. org/10.1016/j.str.2018.03.011 (2018). NEW! Open Design Upright Microscope Simple coarse height adjustment Built-in motorized focus In vivo and In vitro experimentation on one setup OCC or DIC transmitted light (LED) Epi-u fl orescent imaging Uses standard Olympus objectives BOB The Sutter BOB – designed to eliminate the conventional microscope frame – is a versatile, open-design upright microscope platform ideal for slice electrophysiology, widefield fluorescent imaging, two-photon imaging, photostimulation and new techniques just being developed! PHONE: 415.883.0128 | FA X: 415.883.0572 EMAIL: INFO@SUT TER.COM | W W W.SUT TER.COM Nature Methods | VOL 15 | JUNE 2018 | 403–409 | www.nature.com/naturemethods © 2018 Nature America Inc., part of Springer Nature. All rights reserved.

Journal

Nature MethodsSpringer Journals

Published: May 31, 2018

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