CATH Introduction – BioInformatics


What is CATH?

Cath is a database of manually curated protein domain structures. It’s a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy:

  • Class – structures are classified according to their secondary structure composition (mostly alpha, mostly beta, mixed alpha/beta or few secondary structures).
  • Architecture – structures are classified according to their overall shape as determined by the orientations of the secondary structures in 3D space but ignores the connectivity between them.
  • Topology (fold family) – structures are grouped into fold groups at this level depending on both the overall shape and connectivity of the secondary structures.
  • Homologous superfamily – this level groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous.

Cath Domain

structure Domains are regions of contiguous polypeptide chain that have been described as compact, local, and semi-independent units. Within a protein, domains can be anything from independant globular units joined only by a flexible length of polypeptide chain, to units which have a very extensive interface. There are a number of algorithms that have been developed to detect domains automatically, some of which have been incorporated into the CATH update protocol. Many domains, however, still …

Back to school

Finally I am doing MSc. I didn’t do quite well in BEng as I hoped. I didn’t listen to my lecturer at the time.

You can’t look after anyone else if you don’t look after your self

Those were her exact words and something that failed to listen at the time but never forget any more. It’s been haunting me forever. Hopefully MSc in BioInformatics would allow me to put that right. Leave the nightmare behind.

I think I was quite lucky to get in to MSc. I got  ripped apart in my interview. My references came in very late. I am still not properly enrolled because I am waiting for the documents to come through. So I got to make the most of this. But this would be just the beginning.  2 evenings per week (learn Unix, Perl and Java). It’s going to be fun. Brings back some some bad memories and some good memories. Oh and I am totally not using the MSc as an excuse to break my bank to buy one of those Alienware :D.

In the coming weeks I will be putting up the Tutorials I’ve learnt here. Mainly as a personal record and also hope it would be use to someone.