Limits...
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.

Show MeSH
Two new custom rendering options on the Jmol /JSmol page demonstrated using PDB ID 1OQ5 (Celecoxib bound to Carbonic Anhydrase II) (41). (a) Rendering of the crystal packing (3 × 3 unit cells in the ab plane), carbonic anhydrase II (cartoon style) and Celecoxib (CPK style). (b) Jmol rendering of the Celecoxib (ball-and-stick style) in carbonic anhydrase II binding site (stick style). The trimmed ligand VDW surface is color-coded by the distance of the surface to the nearest side chain atom (short contact distances, red; optimal hydrophobic interaction distances, green; longer distances, blue). The red regions (close contacts) at the top of the surface represent hydrogen bonds and metal coordination of the sulfonamide group of Celecoxib with THR 199 and Zinc.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383988&req=5

Figure 4: Two new custom rendering options on the Jmol /JSmol page demonstrated using PDB ID 1OQ5 (Celecoxib bound to Carbonic Anhydrase II) (41). (a) Rendering of the crystal packing (3 × 3 unit cells in the ab plane), carbonic anhydrase II (cartoon style) and Celecoxib (CPK style). (b) Jmol rendering of the Celecoxib (ball-and-stick style) in carbonic anhydrase II binding site (stick style). The trimmed ligand VDW surface is color-coded by the distance of the surface to the nearest side chain atom (short contact distances, red; optimal hydrophobic interaction distances, green; longer distances, blue). The red regions (close contacts) at the top of the surface represent hydrogen bonds and metal coordination of the sulfonamide group of Celecoxib with THR 199 and Zinc.

Mentions: Co-crystal structures of drugs available in the PDB offer atomic level views of drug-macromolecule interactions. We provide visualization tools to help examine these interactions. Each PDB structure has an associated Structure Summary page. If a structure contains ligands, they are enumerated in the Ligand Chemical Component section (Figure 3a) of the Structure Summary page, PDB ID 1OQ5 (41). Ligand analysis options include a 2D ligand interaction diagram generated by PoseView (42) (Figure 3b), interactive 3D binding site views using Ligand Explorer (33) (a Java Webstart application automatically installed and updated on client machines) and Jmol applet (27) (Figure 4b). Ligand Explorer provides options to display hydrogen bonds, metal coordination, hydrophobic contacts, plus solid, mesh and dotted binding site surfaces colored for hydrophobicity.


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)

Two new custom rendering options on the Jmol /JSmol page demonstrated using PDB ID 1OQ5 (Celecoxib bound to Carbonic Anhydrase II) (41). (a) Rendering of the crystal packing (3 × 3 unit cells in the ab plane), carbonic anhydrase II (cartoon style) and Celecoxib (CPK style). (b) Jmol rendering of the Celecoxib (ball-and-stick style) in carbonic anhydrase II binding site (stick style). The trimmed ligand VDW surface is color-coded by the distance of the surface to the nearest side chain atom (short contact distances, red; optimal hydrophobic interaction distances, green; longer distances, blue). The red regions (close contacts) at the top of the surface represent hydrogen bonds and metal coordination of the sulfonamide group of Celecoxib with THR 199 and Zinc.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Two new custom rendering options on the Jmol /JSmol page demonstrated using PDB ID 1OQ5 (Celecoxib bound to Carbonic Anhydrase II) (41). (a) Rendering of the crystal packing (3 × 3 unit cells in the ab plane), carbonic anhydrase II (cartoon style) and Celecoxib (CPK style). (b) Jmol rendering of the Celecoxib (ball-and-stick style) in carbonic anhydrase II binding site (stick style). The trimmed ligand VDW surface is color-coded by the distance of the surface to the nearest side chain atom (short contact distances, red; optimal hydrophobic interaction distances, green; longer distances, blue). The red regions (close contacts) at the top of the surface represent hydrogen bonds and metal coordination of the sulfonamide group of Celecoxib with THR 199 and Zinc.
Mentions: Co-crystal structures of drugs available in the PDB offer atomic level views of drug-macromolecule interactions. We provide visualization tools to help examine these interactions. Each PDB structure has an associated Structure Summary page. If a structure contains ligands, they are enumerated in the Ligand Chemical Component section (Figure 3a) of the Structure Summary page, PDB ID 1OQ5 (41). Ligand analysis options include a 2D ligand interaction diagram generated by PoseView (42) (Figure 3b), interactive 3D binding site views using Ligand Explorer (33) (a Java Webstart application automatically installed and updated on client machines) and Jmol applet (27) (Figure 4b). Ligand Explorer provides options to display hydrogen bonds, metal coordination, hydrophobic contacts, plus solid, mesh and dotted binding site surfaces colored for hydrophobicity.

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