[Protein-crystallography] PDBe introduces PDBeXpress - easy-to-use
yet powerful PDB analysis tools
Gerard DVD Kleywegt
(by gerard from xray.bmc.uu.se)
Thu Aug 18 12:01:47 EST 2011
As part of its recent summer update, the Protein Data Bank in Europe (PDBe;
http://pdbe.org) introduced PDBeXpress (http://pdbe.org/express), an umbrella
name for a set of easy-to-use yet powerful PDB analysis tools. The first two
modules can be used to answer questions such as "what residues are found in the
binding sites of vitamin B1?" and "given that I have a cavity lined with Asp,
Trp, Ile, Val and His, what compounds are known to bind to such a set of
There are many advanced tools and resources available worldwide to search,
browse and analyse the contents of the PDB at the level of entire entries or
molecules. However, when it comes to the nitty-gritty of analysing the core
structural data contained in the PDB, i.e. atoms and their interactions, the
situation is different. PDBeMotif (http://pdbe.org/motif) is one of the most
powerful services available (freely) for analysing PDB entries in terms of
detailed structure, sequence and chemistry. A practical example is described
However, PDBeMotif is also quite complex to use. For this reason, PDBe has
begun to develop small modules of PDBeMotif (and other) analysis functionality
that are presented in such a way that they are very easy to use by non-experts
and provide answers to common but complex questions. The first two PDBeXpress
modules were released in the recent PDBe summer update; both provide
information and statistics about ligands in the PDB. They can be accessed from
http://pdbe.org/express (help and documentation are available from there as
What residues interact?
For any ligand in the PDB that you specify, this tool (using PDBeMotif behind
the scenes) will retrieve the residues with which this ligand interacts, as
observed in current 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 further analyses using PDBeMotif.
When you start the service, all you need to provide is the name or 3-letter
code of the compound of interest (or do a search at PDBeChem -
http://pdbe.org/chem - if you are unsure). You can select your favourite
compound, or compare closely related compounds such as GBC, GLC and GLO.
The results page contains a graph that shows the relative occurrence of the
amino acids in the binding sites of the compound (extracted from the PDBeMotif
database). If you hover your mouse over the bars, you see the total number of
interactions between a residue type and your compound. If you click on a bar,
you will get more details (e.g., "15.6% of the total interactions are with ASP
(16 interactions with 9 occurrences of GLO in 7 PDB entries)"). Below this are
links that take you to the corresponding PDB entries or further analyses using
What binds here?
This tool enables you to search for ligands in the PDB that interact with a
given set of residues and the results are also shown in an interactive graph.
When you use this tool, you simply click on the amino-acid types that are
present in the binding site. If you require that a residue occurs twice, click
it twice, etc. For instance, what do you think is the most frequently found
compound to interact with "ARG ARG ARG LYS LYS LYS"?
We hope that you will find PDBeXpress useful. As always, we welcome
constructive criticism, comments, suggestions, bug reports, etc. through the
feedback button at the top of any PDBe web page. We also welcome your
suggestions for future PDBeXpress modules!
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_admin from ebi.ac.uk
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