Representation of viruses in the remediated PDB archive

Lawson, Catherine L.; 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:1625657

Lawson, Catherine L. ^[1]; Dutta, Shuchismita ^[2]; Westbrook, John D. ^[2]; Henrick, Kim ^[3]; Berman, Helen M. ^[2]

Rutgers Univ., Piscataway, NJ (United States). RCSB Protein Data Bank and Dept. of Chemistry and Chemical Biology; DOE/OSTI
Rutgers Univ., Piscataway, NJ (United States). RCSB Protein Data Bank and Dept. of Chemistry and Chemical Biology
European Molecular Biology Lab. (EMBL), Cambridge (United Kingdom). Macromolecular Structure Database- European Bioinformatics Inst.

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.

Research Organization:: Univ. of Washington, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation (NSF); National Institute of General Medical Sciences (NIGMS); National Library of Medicine (NLM); National Cancer Institute (NCI); National Center for Research Resources (NCRR); National Institute of Biomedical Imaging and Bioengineering (NIBIB); National Institute of Neurological Disorders and Stroke (NINDS); Wellcome Trust; European Union; Biotechnology and Biological Sciences Research Council (BBSRC); Medical Research Council (MRC); National Center for Research Resources

Grant/Contract Number:: FG02-00ER41132

OSTI ID:: 1625657

Alternate ID(s):: OSTI ID: 22347978

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

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
Protein Data Bank
biochemistry & molecular biology
biological assemblies
biophysics
crystallography
database integration
helical symmetry
point symmetry
uniform curation
virus structures

Representation of viruses in the remediated PDB archive

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