[Protein-crystallography] PDBe introduces PDBeXpress - easy-to-use yet powerful PDB analysis tools

Gerard DVD Kleywegt via xtal-log%40net.bio.net (by gerard from xray.bmc.uu.se)
Thu Aug 18 12:01:47 EST 2011


Hi all,

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 
residues?"

-----

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 
here: 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Structural_motifs_in_the_PDB

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 
well).


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 
PDBeMotif.


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

---
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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