Oliver Testa's Research Page

CCPLUS - The new coiled-coil database

The aims of my research:

The new coiled-coil database

Coiled-coil structures can be identified using an algorithm called SOCKET. This algorithm looks for specific packing found in coiled coils, and reports a wealth of structural information. This data has been compiled into a coiled-coil database before, but this is out-of-date and difficult to use. I have used this algorithm to scan and identify all the coiled-coil structures in the Brookhaven Protein Data Bank and PQS databases. The results of these scans have been organized and stored for use in my research.

The tool I have developed is called CCPLUS. It is a relational database which holds information about every aspect of coiled-coil structures identified by SOCKET. This data is stored heirarchically; One protein can contain many coiled coils, one coiled coil has multiple helices, each helix has many residues. Some of these residues then interact forming 'Knobs-into-holes' packing (Crick, F. H. C. [1953] Acta Crystallographica, 6, 689-697).

How coiled-coil information is organized

2BRI illustrating different levels of coiled-coil structural information.

Visualizing coiled coils

I have also created a program to manage data in the CCPLUS database and create scripts to render these structures with PYMOL. This method of visualization was developed in conjunction with Fay. A script has been created for every coiled-coil structure that SOCKET has identified. These scripts use specific styles and colours to highlight coiled coils and their interactions, and can render structures within seconds of getting results from CCPLUS.

Pymol scripts help visualize coiled coils

2ZTA illustrating how coiled coils are visualized using PYMOL scripts.

Using the new coiled-coil database

This database is already being used to answer questions about the sequence-to-structure rules by which coiled-coils assemble. Fay is using the database to study coiled-coil topologies. Beth is using the database in her research into switching peptides. There are currently several other collaborations using the database, and every bit of feedback I receive goes into developing and improving this tool.

Latest News: The CC+ database is now available to the public! Please let me know if you have any queries, feedback or bug reports.

Other bits...

I also handle the lab website (thanks, Steve!) here at Bristol. This site was designed to replicate the venerable styles of the Bristol School of Chemistry sites, but has subtle differences because everything you see here I have coded from scratch using standards-compliant XHTML1.1 and CSS. You can check this by visiting the links in the footers of this site.

XHTML is a strict form of markup proposed by the W3C, and because it is modular it is nice and easy to update. CSS is a way of separating the information in a web page and the styles describing how that data is displayed and styled. What this means is that I have tried to make this site compatible with as many browsers and screen-reading technologies as I can. I've tested it on IEwin 5/6, IEmac 5, Opera 8 and good ol' Firefox, but if you manage to spot a bug that I haven't feel free to let me know :)

Finally, the following sources were invaluable when learning how to make these pages, and I'm very grateful to the people out there making tutorials for the rest of us.