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PDBeXpress is a collection of tools that extract and present useful information and statistics from the PDB using PDBe services and resources such as PDBeMotif. These tools have a simple interface with minimal input. They can be accessed through the navigation panel on the left and are briefly described below (use the Documentation link for more detailed descriptions).


New functionality will be added in the future. If you have requests or comments, please use the feedback option at the top of this page.


The following tools are currently available as part of PDBeXpress:

Ligands

At present, there are three tools that provide information and statistics about ligands in the PDB.

What residues interact?

For any ligand in the PDB, this tool will retrieve the residues with which this ligand interacts, as observed in PDB entries. The results are plotted on an interactive graph, which can be used to further view the PDB entries in which the interactions occur, or to perform advanced analyses using PDBeMotif. The results can be further refined by selecting a Pfam or CATH domain. By applying this filter, only interacting residues which belong to the selected domain are retrieved.

What binds here?

This tool enables you to search for ligands in the PDB that interact with a given set of residues (e.g. "HIS ASP SER") and the results are plotted on an interactive graph. This graph links to PDB entries containing the interactions, as well as advanced analysis options within PDBeMotif.

Which enzymes interact?

For any ligand in the PDB, this tool will retrieve the enzymes with which this ligand interacts, as observed in PDB entries. The results are plotted on an interactive graph, which can be used to drill down to deeper levels of EC, or to view the PDB entries in which the interactions occur.