Representation of viruses in the remediated PDB archive

Dutta, Shuchismita; Westbrook, John D.; Henrick, Kim; Berman, Helen M.

doi:10.1107/S0907444908017393

Representation of viruses in the remediated PDB archive

Journal Article · Fri Aug 01 00:00:00 EDT 2008 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S0907444908017393· OSTI ID:22347978

Dutta, Shuchismita; Westbrook, John D. ^[1]; Henrick, Kim ^[2]; Berman, Helen M. ^[1]

RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087 (United States)
Macromolecular Structure Database-European Bioninformatics Institute, EMBL Outstation-Hinxton, Cambridge CB10 1SD (United Kingdom)

A new data model for PDB entries of viruses and other biological assemblies with regular noncrystallographic symmetry is described. A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.

OSTI ID:: 22347978

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography, Journal Name: Acta Crystallographica. Section D: Biological Crystallography Journal Issue: Pt 8 Vol. 64; ISSN ABCRE6; ISSN 0907-4449

Country of Publication:: Denmark

Language:: English

Cited By (13)

A Multiscale Model for Virus Capsid Dynamics Chen, Changjun; Saxena, Rishu; Wei, Guo-Wei International Journal of Biomedical Imaging, Vol. 2010 https://doi.org/10.1155/2010/308627	journal	January 2010
Analytical models of icosahedral shells for 3D optical imaging of viruses Jafarpour, Aliakbar arXiv https://doi.org/10.48550/arxiv.1408.1582	preprint	January 2014
RCSB Protein Data Bank: sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education Zardecki, Christine; Berman, Helen M.; Christie, Cole Acta Crystallographica Section A Foundations and Advances, Vol. 74, Issue a1 https://doi.org/10.1107/s0108767318098811	journal	July 2018
Trendspotting in the Protein Data Bank Berman, Helen M.; Coimbatore Narayanan, Buvaneswari; Costanzo, Luigi Di FEBS Letters, Vol. 587, Issue 8 https://doi.org/10.1016/j.febslet.2012.12.029	journal	January 2013
Structure of the Pandemic Kearns, Sarah Structure, Vol. 28, Issue 8 https://doi.org/10.1016/j.str.2020.07.007	journal	August 2020
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang Database, Vol. 2018 https://doi.org/10.1093/database/bay002	journal	January 2018
Outcome of the First Electron Microscopy Validation Task Force Meeting Henderson, Richard; Sali, Andrej; Baker, Matthew L. Structure, Vol. 20, Issue 2 https://doi.org/10.1016/j.str.2011.12.014	journal	February 2012
EMDataBank unified data resource for 3DEM Lawson, Catherine L.; Patwardhan, Ardan; Baker, Matthew L. Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1126	journal	November 2015
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1004	journal	October 2018
Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB) Adams, Paul D.; Afonine, Pavel V.; Baskaran, Kumaran Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 4 https://doi.org/10.1107/s2059798319004522	journal	April 2019
EMDataBank.org: unified data resource for CryoEM Lawson, C. L.; Baker, M. L.; Best, C. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq880	journal	October 2010
Investigation of core structure and stability of human Pyruvate Dehydrogenase complex: A coarse-grained approach Hezaveh, Samira; Zeng, An-Ping; Jandt, Uwe ACS https://doi.org/10.15480/882.1498	journalarticle	January 2017
Principles and characteristics of biological assemblies in experimentally determined protein structures Xu, Qifang; Dunbrack, Roland L. Current Opinion in Structural Biology, Vol. 55 https://doi.org/10.1016/j.sbi.2019.03.006	journal	April 2019

Similar Records

Representation of viruses in the remediated PDB archive

Journal Article · Fri Aug 01 00:00:00 EDT 2008 · Acta Crystallographica. Section D: Biological Crystallography · OSTI ID:1625657

Remediation of the protein data bank archive

Journal Article · Mon Dec 10 23:00:00 EST 2007 · Nucleic Acids Research · OSTI ID:1625433

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
CRYSTALS
MATRICES
PROTEINS
SYMMETRY
TRANSFORMATIONS

Representation of viruses in the remediated PDB archive

Citation Formats

Cited By (13)

Similar Records

Related Subjects