The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
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.
Affiliation: RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA email@example.com.Show MeSH
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.
Affiliation: RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA firstname.lastname@example.org.