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Autosuggestions from a Simple Search for actinomycin

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Advanced Search options for querying BIRD

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BIRD widget from PDB ID 1a7y

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

Simple Search
Biologically interesting Molecules from BIRD can be searched by typing a name (vancomycin), a BIRD ID (PRD_000204), type (glycopeptide), or class (antibiotic) in the top search bar. Suggestions will appear under the BIRD Molecules category.

Advanced Search
Biologically interesting Molecules from BIRD can also be searched from the advanced search menu.  Search by text/name, BIRD type (structural classification of the molecule), or BIRD class (broad definition of the molecule function).

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.

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Protein Workshop view of actinomycin D as seen in PDB ID 1a7y.

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Ligand Explorer view of Vancomycin PRD_000204.

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Protein Workshop view of vancomycin PRD_000204 as seen in PDB ID 1pnv.

Visualize BIRD Molecules

Ligand Explorer

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.

Protein Workshop

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.