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The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Rose PW, Prlić A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK - Nucleic Acids Res. (2014)

Bottom Line: Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web.We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations.Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.

View Article: PubMed Central - PubMed

Affiliation: RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA pwrose@ucsd.edu.

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Gene view of human chromosome 16, zoomed into the region of the HBA1, hemoglobin α1 gene. The top of the view is a ruler that shows the current region along a chromosome. The blue/red/green/black colored tracks is the color-coding of the nucleotides. The PDB track shows two PDB chains: PDB ID 2W72 chain A (50), PDB ID 1C7C chain A (51) and how they align to this region on the chromosome. The Genes track shows four transcripts, one of which is the main HBA1 coding sequence. By zooming out, the human α globin gene cluster, spanning about 30 kb and including several hemoglobin genes, can be visualized.
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Figure 6: Gene view of human chromosome 16, zoomed into the region of the HBA1, hemoglobin α1 gene. The top of the view is a ruler that shows the current region along a chromosome. The blue/red/green/black colored tracks is the color-coding of the nucleotides. The PDB track shows two PDB chains: PDB ID 2W72 chain A (50), PDB ID 1C7C chain A (51) and how they align to this region on the chromosome. The Genes track shows four transcripts, one of which is the main HBA1 coding sequence. By zooming out, the human α globin gene cluster, spanning about 30 kb and including several hemoglobin genes, can be visualized.

Mentions: To enable better integration between the growing corpus of genomic data and 3D information in the PDB, we implemented a pipeline that maps protein structure data onto the human genome. We can now link most human PDB entries to their corresponding genes. To visualize this mapping, we created Gene View to support browsing of the human genome with PDB data mapped onto corresponding genomic positions. These data can be correlated with other genomic annotations, such as gene structure prediction, DNA repeats or sequence conservation, across ∼50 vertebrate genomes. Our graphical view is built atop the BioDalliance genome browser (49). Users can ‘mouse’ through the region around a human gene, as shown in the Gene View (Figure 6), PDB ID 2W72 chain A (50), PDB ID 1C7C chain A (51).


The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Rose PW, Prlić A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK - Nucleic Acids Res. (2014)

Gene view of human chromosome 16, zoomed into the region of the HBA1, hemoglobin α1 gene. The top of the view is a ruler that shows the current region along a chromosome. The blue/red/green/black colored tracks is the color-coding of the nucleotides. The PDB track shows two PDB chains: PDB ID 2W72 chain A (50), PDB ID 1C7C chain A (51) and how they align to this region on the chromosome. The Genes track shows four transcripts, one of which is the main HBA1 coding sequence. By zooming out, the human α globin gene cluster, spanning about 30 kb and including several hemoglobin genes, can be visualized.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383988&req=5

Figure 6: Gene view of human chromosome 16, zoomed into the region of the HBA1, hemoglobin α1 gene. The top of the view is a ruler that shows the current region along a chromosome. The blue/red/green/black colored tracks is the color-coding of the nucleotides. The PDB track shows two PDB chains: PDB ID 2W72 chain A (50), PDB ID 1C7C chain A (51) and how they align to this region on the chromosome. The Genes track shows four transcripts, one of which is the main HBA1 coding sequence. By zooming out, the human α globin gene cluster, spanning about 30 kb and including several hemoglobin genes, can be visualized.
Mentions: To enable better integration between the growing corpus of genomic data and 3D information in the PDB, we implemented a pipeline that maps protein structure data onto the human genome. We can now link most human PDB entries to their corresponding genes. To visualize this mapping, we created Gene View to support browsing of the human genome with PDB data mapped onto corresponding genomic positions. These data can be correlated with other genomic annotations, such as gene structure prediction, DNA repeats or sequence conservation, across ∼50 vertebrate genomes. Our graphical view is built atop the BioDalliance genome browser (49). Users can ‘mouse’ through the region around a human gene, as shown in the Gene View (Figure 6), PDB ID 2W72 chain A (50), PDB ID 1C7C chain A (51).

Bottom Line: Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web.We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations.Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.

View Article: PubMed Central - PubMed

Affiliation: RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA pwrose@ucsd.edu.

Show MeSH