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. 2006 Jan 1;34(Database issue):D302-5.
doi: 10.1093/nar/gkj120.

The RCSB PDB information portal for structural genomics

Andrei Kouranov  1 , Lei Xie, Joanna de la Cruz, Li Chen, John Westbrook, Philip E Bourne, Helen M Berman
Affiliations

The RCSB PDB information portal for structural genomics

Andrei Kouranov et al. Nucleic Acids Res. .

Abstract

The RCSB Protein Data Bank (PDB) offers online tools, summary reports and target information related to the worldwide structural genomics initiatives from its portal at http://sg.pdb.org. There are currently three components to this site: Structural Genomics Initiatives contains information and links on each structural genomics site, including progress reports, target lists, target status, targets in the PDB and level of sequence redundancy; Targets provides combined target information, protocols and other data associated with protein structure determination; and Structures offers an assessment of the progress of structural genomics based on the functional coverage of the human genome by PDB structures, structural genomics targets and homology models. Functional coverage can be examined according to enzyme classification, gene ontology (biological process, cell component and molecular function) and disease.

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Figures

Figure 1
Figure 1
August 2005 report from the structural genomics information portal showing structural genomics structures with sequence similarity <30% relative to solved structures in the PDB by year. Sequence comparisons are performed using the blastclust application (7).
Figure 2
Figure 2
Normalized functional coverage of the human genome by sequence (from Ensembl; red), by structures from the PDB (blue), by structural genomics targets (green) and homology models from SUPERFAMILY (yellow). When viewing the figure from the online structural genomics portal, clicking on the appropriate bar of the histogram will produce a list of sequences or structures that define the distribution.
See this image and copyright information in PMC

References

    1. Berman H., Henrick K., Nakamura H. Announcing the worldwide Protein Data Bank. Nature Struct. Biol. 2003;10:980. - PubMed
    1. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. - PMC - PubMed
    1. Chen L., Oughtred R., Berman H.M., Westbrook J. TargetDB: a target registration database for structural genomics projects. Bioinformatics. 2004;20:2860–2862. - PubMed
    1. Doreleijers J.F., Mading S., Maziuk D., Sojourner K., Yin L., Zhu J., Markley J.L., Ulrich E.L. BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank. J. Biomol. NMR. 2003;26:139–146. - PubMed
    1. Xie L., Bourne P.E. Functional coverage of the human genome by existing structures, structural genomics targets, and homology models. PLoS Comput. Biol. 2005;1:e31. - PMC - PubMed

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