Posted by: woodforthetrees | February 19, 2010

Why would I use the Structural Genomics Knowledgebase and not the PDB?

Structural Genomics Knowledgebase

The Structural Genomics Knowledgebase is not a rival to the PDB.

I’m asked this question a lot, and I hope to try and explain it a bit here. It’s worth noting before we start that the Structural Genomics Knowledgebase and the RCSB PDB have the same director, and so they are designed to complement rather than rival.

The PDB, or Protein Data Bank, is primarily an archive that holds information about the three-dimensional structures of biological molecules. It initially held only protein structures, but now it has nucleic acid structures too. It also contains some basic information on the methods used to solve the structure and links to related publications. If you’re asking a specific structural question, then start with the PDB.

The Structural Genomics Knowledgebase is a web portal that brings together information from multiple databases and sources into one place. Instead of having to enter your protein sequence into lots of databases you just enter it once. If you’re asking a general question about a protein then this is the right place to start.

A search of the Structural Genomics Knowledgebase gives you information on:

  • Any structures in the PDB
  • Links to Protopedia and many other databases
  • Any existing protein models (mainly from SwissProt)
  • Whether one of the structural genomics groups is working on the structure
  • How much progress has been made on the structure
  • Detailed cloning, expression and purification protocols
  • Where to get hold of clones containing the gene to express the protein
  • Recent methods that have been developed
  • Information on all the technology developed by the Protein Structure Initiative
  • Structures that have been highlighted by Nature Publishing Group

It’s one of the new generation of data services that I think Don Tapscott and Anthony Williams refer to in their book Wikinomics:

Scientists are using Web services to revolutionize the way they extract and interpret data from different sources, and to create entirely new data services…. Imagine you had the power to weave together all the latest data on [a] species from all the world’s biological databases with just one click. It’s not far-fetched. That power is here, today.

To my mind, the challenges in creating a useful data service are two-fold: one, there are the technical issues of how to share the data; two, there is the question is how best to present so much data without making it overwhelming. Web portals and web services are evolving all the time as we learn how best to present and share data.

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