Charles mostly works in the field of computation chemistry. He is investigating interactions between molecules (eg between a section of DNA and a protein) by generating simulations of the interaction, and mining these for information.

To do this, he uses off-the shelf software to generate movie files of molecules interacting, and then uses custom analysis software to investigate these.

In his normal work, Charles doesn't regularly use bioinformatics. He is involved with two projects that do use some bioinformatics, and he described them to me.

biosimgrid

www.biosimgrid.org

biosymgrid aims to provide tools for manipulation and storage of (bio)molecular simulation data using distributed resources. This is useful, as terrabytes of data are currently produces by the molecular simulation community and then discarded (or at least no shared). Part of the biosimgrid project aims to use bioinformatics resources to generate annotation of molecules involved in the simulation, eg look up the secondary structure of a given protein etc

allergens project

Charles is working with Ruta Furmonaviciene, trying to understand why particular proteins are allergens. They are working on the hypothesis that this is due to the structure of the protein. He has written scripts to cross-reference proteins which are known allergens and stored in a database. These scripts are attached to this page.

Proteins are stored in the database as SWISS-PROT references. Charles scripts fetch a particular SWISS-PROT reference, look up the protein family of the protein in one database, look up known or predicted structures in other databases and insert and insert this collected information into the protein database. Charles tried to automate this process, but found it difficult. He was interested in Taverna as a tool for automating the process.

Suggested next steps

Charles suggested a biosimgrid/mygrid meeting to find common themes.