Dr Alison Cuff

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

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 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 here )

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.

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.

The Protein Chart is published by Wiley and can be purchased here ( here)

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

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