CATH

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== Dr Alison Cuff ======


{{  :cathteam:meandtoby.jpg| Me and my Cat}}

===== CATH Manager =====

I am responsible for the general management and manual curation of CATH.

===== Academic Background =====

As a undergraduate, I read for a BSc(Hons) degree in Biomedical Sciences at the University of Durham and then, after deciding I wanted to pursue Bioinformatics research, I took a MSc degree in Information Technology at the University of Teesside (this was all back in the days before MSc courses in Bioinformatics became available!).

My PhD was undertaken at the University of Reading, supervised by Dr Andrew Martin,  and involved developing an automated analysis of the protein p53. P53 is a tumour supressor protein; mutations to this
protein has been shown to be responsible for up to half of all human
cancers. I developed a protocol for analysing single site
mutations in this protein in terms of how they affected its functionality and/or the stability (see [[ http://www.bioinf.org.uk/p53/| here]] for more information)

A significant piece of work during my PhD was the development of the 'CheckHBond'
program, which takes any two residues that are hydrogen bonded within a
protein, mutates one and then calculates if the hydrogen bond is
maintained (see [[ http://www.bioinf.org.uk/hbonds/| here ]])

{{:cathteam:grid.gif|}} 

**The CheckHBond Program.** One residue is chosen as the 'key' residue (in this case the donor). The protein is moved so its in a set 'standard orientation' as defined by the checkhbond algorithm. The other residue (the acceptor) is known as the 'partner' residue. A PARTNERTOACCEPT grid, which stores the location of donor atoms able to hydrogen bond with the  partner residue, is generated and then rotated  such that it is centred around the partner residue. If a hydrogen bond can be formed between the residues then a populated cell in the DONOR grid (which stores the location of the key residues donor atoms) will be concident with a populated cell in the PARTNERTOACCEPT grid.

I joined the CATH group as a postdoctoral researcher in March 2006.

===== Current Research Interests =====

When I haven't been busy with the curation of the CATH database, recent work has focused on investigating the existance of a 'fold
continuum' and the validity of a hierarchical classification
system. Results have shown that, for the most part, CATH superfamilies are
structurally conserved and generally dissimilar to structures in other
fold groups. However, in some of the most highly populated superfamilies, a
considerable amount of structural diversity between relatives has been
observed. Structural overlap between fold groups is limited to a few
architectures that contain small motifs (such as the alpha/beta plait)
which reoccur. A paper describing this work should (hopefully!) be published shortly.

I have also been involved in the creation of an educational tool called the
Protein Chart.

{{:cathteam:chart.png|}}


**The Protein Chart** is published by Wiley and can be purchased here ([[http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527319638.html| here]])

Future work will involve the functional annotation of proteins and
functional classification.

===== Selected Publications =====

{{pubmed>long:11793474}}
{{pubmed>long:15561139}}
{{pubmed>long:16601005}}
{{pubmed>long:17135200}}



===== Other Interests =====

All things film (including making them).I'm also trying to teach myself to knit.



===== Other CATH Team Members =====

~~DIR?cols=page;description&hdrs=Person; Description~~
CATH

User Tools

Site Tools

Page Tools
