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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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Protein feature view for Calmodulin. The main reference (gray track) is the full-length sequence from UniProt. The top of the view (green) provides a summary of important functional motifs plus UniProt sites. By moving the mouse over any of these regions, more information about this region can be viewed. This is followed by annotations from Pfam (yellow), SCOP domain annotations (orange), computationally inferred information, such as protein disorder score or hydropathy. At the bottom, in blue, are the data derived from PDB. A secondary-structure track shows helical and strand regions along the protein. In the ‘condensed’ (default) view representative protein chains are being displayed mapped to the protein sequence. To view the mapping of all available PDB chains the ‘expanded’ view can be called by pressing the ‘+’ button.
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Figure 5: Protein feature view for Calmodulin. The main reference (gray track) is the full-length sequence from UniProt. The top of the view (green) provides a summary of important functional motifs plus UniProt sites. By moving the mouse over any of these regions, more information about this region can be viewed. This is followed by annotations from Pfam (yellow), SCOP domain annotations (orange), computationally inferred information, such as protein disorder score or hydropathy. At the bottom, in blue, are the data derived from PDB. A secondary-structure track shows helical and strand regions along the protein. In the ‘condensed’ (default) view representative protein chains are being displayed mapped to the protein sequence. To view the mapping of all available PDB chains the ‘expanded’ view can be called by pressing the ‘+’ button.

Mentions: For data visualization, so-called ‘tracks’ are used (Figure 5). Color-coding on the left side of the view indicates the provenance of a track, e.g. all information coming from UniProt (44) is in green, PDB information is in blue, etc. In some cases, we are dealing with manually curated information, such as SCOP domains (45). Alternatively, the annotation has been inferred indirectly, as for Pfam domains (46), or calculated, as for hydropathy scores (47) and propensity for protein disorder score based on JRONN (P. Troshin and G. J. Barton, unpublished), a Java implementation of RONN (48).


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)

Protein feature view for Calmodulin. The main reference (gray track) is the full-length sequence from UniProt. The top of the view (green) provides a summary of important functional motifs plus UniProt sites. By moving the mouse over any of these regions, more information about this region can be viewed. This is followed by annotations from Pfam (yellow), SCOP domain annotations (orange), computationally inferred information, such as protein disorder score or hydropathy. At the bottom, in blue, are the data derived from PDB. A secondary-structure track shows helical and strand regions along the protein. In the ‘condensed’ (default) view representative protein chains are being displayed mapped to the protein sequence. To view the mapping of all available PDB chains the ‘expanded’ view can be called by pressing the ‘+’ button.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 5: Protein feature view for Calmodulin. The main reference (gray track) is the full-length sequence from UniProt. The top of the view (green) provides a summary of important functional motifs plus UniProt sites. By moving the mouse over any of these regions, more information about this region can be viewed. This is followed by annotations from Pfam (yellow), SCOP domain annotations (orange), computationally inferred information, such as protein disorder score or hydropathy. At the bottom, in blue, are the data derived from PDB. A secondary-structure track shows helical and strand regions along the protein. In the ‘condensed’ (default) view representative protein chains are being displayed mapped to the protein sequence. To view the mapping of all available PDB chains the ‘expanded’ view can be called by pressing the ‘+’ button.
Mentions: For data visualization, so-called ‘tracks’ are used (Figure 5). Color-coding on the left side of the view indicates the provenance of a track, e.g. all information coming from UniProt (44) is in green, PDB information is in blue, etc. In some cases, we are dealing with manually curated information, such as SCOP domains (45). Alternatively, the annotation has been inferred indirectly, as for Pfam domains (46), or calculated, as for hydropathy scores (47) and propensity for protein disorder score based on JRONN (P. Troshin and G. J. Barton, unpublished), a Java implementation of RONN (48).

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