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[X-plor] Let's GO, with Dora the PDBeXplorer!

Gerard DVD Kleywegt via x-plor%40net.bio.net (by gerard from xray.bmc.uu.se)
Thu Mar 1 14:36:33 EST 2012

Hi all,

As you may recall, the Protein Data Bank in Europe (PDBe; http://pdbe.org) has 
launched a number of PDB archive browsers in the past two years. These allow 
users to explore and analyse what is in the PDB based on concepts and 
classifications they are familiar with, such as the EC system, chemical 
compounds, taxonomy or amino-acid sequences (see http://pdbe.org/browse for 
more information).

The most recent addition is a browser that is based on the GO system 
(http://pdbe.org/go). GO stands for Gene Ontology, a major bioinformatics 
initiative with the aim of standardizing the representation of gene and gene 
product attributes across species and databases (http://geneontology.org/). 
The SIFTS project (http://pdbe.org/sifts) maps GO annotations from UniProt to 
all proteins and protein fragments that occur in the PDB. These GO terms 

* molecular function, the elemental activities of a gene product at the 
molecular level (e.g., catalysis of free radical formation)

* cellular component, the localisation of a gene product in a cell or its 
extracellular environment (e.g., outer membrane-bounded periplasmic space)

* biological process, operations or sets of molecular events with a defined 
beginning and end, pertinent to the functioning of integrated living units: 
cells, tissues, organs, and organisms (e.g., neuron apoptosis)

To start exploring, surf to http://pdbe.org/go

In the left panel you can either:

- click on one of the three examples and then hit the Submit button

- start exploring the GO classification by expanding the molecular_function, 
cellular_component or biological_process term. Clicking on any of these will 
expand the classification to show the underlying terms, and these can be 
clicked on for further drilling. If a term is shown on a grey background, it 
means that there are no proteins in the PDB that have been annotated with that 

- start typing a term in the input box (above the Submit button). Once you 
have typed a few characters, an auto-complete function will show you a list of 
all the matching GO terms. Select any one of these and hit the Submit button.

Once you have selected a GO term that is of interest to you, the browser will 
load all PDB entries that contain a protein (fragment) that has been annotated 
with that term in the central panel of the browser. (The right panel contains 
more information about the GO term and how it fits in the GO classification - 
click on the image to get a bigger version.) In the central panel, the "PDB 
entries" tab shows a simple list of the PDB entries. However, there are other 
tabs that provide different views on this set of entries, such as:

- which ligands are found in these entries?

- what folds are represented (CATH)?

- what quaternary structures occur (PISA)?

- what sequence families are present (Pfam)?

- from which taxa have structures been determined?

- who has determined these structures?

For instance, if your are interested in "purine nucleotide biosynthetic 
process", you may find that:

- there are 310 relevant structures in the PDB

- the most common ligands are Mg, SO4, PO4, GDP, K, CL, AMP and ADP

- the structures are mostly of the alpha/beta type (82%), with 45% of all 
domains adopting a 3-layer ABA sandwich fold

- 70% of the entries contain homo-oligomeric structures (and 50% of those are 
homodimers, but there are also 5 homohexameric structures)

- the set of entries covers 43 different Pfam families

- there are 11 proteins in 5 distinct entries from Yersinia pestis

- R.B. Honzatko is the most prolific depositor of PDB entries in this category 
(useful to know if you are looking for collaborators or referees)

As you can see, the GO browser can be used to explore many aspects of what is 
known in terms of 3D structures for proteins with a given function, role or 

If you have any questions, comments or suggestions, please use the button 
marked "FEEDBACK" in the top right corner of any PDBe webpage.

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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