Searching and visualising data from PDBe

Basic searches: With PDBeView you can perform simple searches based on a PDB code, keyword, author name(s), ligand names or code, or any piece of text. The query can be restricted to specific types of experiments (crystallography, NMR or electron microscopy, for example), species, or to a particular range of resolutions. You can also use sequence information to search for structures with closely matching sequences.

Structure comparisons: PDBeFold allows you to identify structures that are similar to that of a reference protein. Pairwise or multiple comparisons as well as 3D alignments of structures can be performed.

Ligands and their binding sites: PDBeChem allows you to search for and visualise any molecule in the PDB’s ligand dictionary using keywords, PDB codes, SMILES strings (stereo or non-stereo), fragments or fingerprints. You can use the PDBeMotif search interface to query ligand-binding sites and their geometry or the statistics of ligand-binding sites.

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Motif-based searches: PDBeMotif allows complex searches of the PDB based on small 3D motifs, sequence motifs in conjunction with ligand environment, secondary structure patterns (such as helix–turn–helix motifs), Prosite patterns and combinations of torsion angles and catalytic sites. PDBeMotif also allows you to search by sequence and perform multiple alignments of sequences or structures.

Browser of structural knowledge: PDBeXplore allows you to browse the structural knowledge embodied in the PDB based on classification systems that are familiar to molecular biologists, biochemists and other life scientists including Enzyme Class, CATH domains, Pfam families, sequence and chemical compounds.