Search, View Annotations, and Visualize Peptide-like Antibiotic and Inhibitor Molecules
BIRD refers to the wwPDB's Biologically Interesting Molecule Reference Dictionary, and contains information about the representation of peptide-like antibiotic and inhibitor molecules in the PDB archive.
An example of a BIRD molecule is April's Molecule of the Month: actinomycin.
New RCSB PDB website features utilize BIRD data to provide improved searching and visualization options for these molecules:
Search BIRD Molecules
View Annotations from BIRD
The BIRD widget on an entry's Structure Summary page will display the ID, image, name, type, class, and chain location for any such molecules in the entry. Ligand Explorer can be launched to view the molecule and binding site in 3D.
As with other Structure Summary page features, the examples displayed (ID, name, type, and class) can be used to find other PDB entries with the same characteristics.
Visualize BIRD Molecules
Ligand Explorer can be launched from the BIRD Widget to visualize these molecules and their binding sites. The program can center on other molecules by clicking on a name or identifier from the left hand menu. Intermolecular interactions such as hydrogen bond or hydrophobic interactions and a binding site surface can be turned on for the active ligand.
In Protein Workshop, BIRD molecules are listed in the right hand menu and can be manipulated as with any other macromolecule chain or ligand. Protein Workshop can be launched from any entry's Structure Summary page.