1.3 E-malaria  (Page 2/3)

To supply the docking engine we originally built software to enable molecules to be drawn and converted from a 2D sketch to a 3D model with a realistic molecular conformation using empirical rules and molecular mechanics and semi-empirical quantum codes. The drug target for the initial studies was the DHFR protein, chosen for the different way the DHFR protein is regulated in mosquitoes and humans, which makes it very suitable as a target to block. The structure of the DHFR protein was obtained from the protein data bank (PDB) and a scoop suitable for docking produced.

The scripts developed set up the computational job, bringing together the molecule submitted by the user with the drug target, and then submitted the job to the UD system. Web interfaces were provided to keep track of the individual’s runs and allowed the 2D, 3D molecular and docked structures to use the very versatile Java based Jmol program . Keeping track of structures and results for each user required some system to identify the users. We were careful to collect no personal information as we had to be sure that we were clear of any data protection requirements, especially in regard to those users who might be under 18 years of age. In subsequent use for undergraduate teaching we linked the eMalaria system to the University (LDAP) authentication system, allowing access to designated students.

The site was designed to be as accessible as possible for students with special educational needs, particularly those with dyslexia. Information is presented in manageable amounts and boxed away from the navigation tools to avoid confusion. The website has been designed to use cascading style sheets (CSS) to allow students to pick the text font, colour and background that makes it easiest for them to read the website. At all times the user’s built in browser settings are able to override the standard website style sheet. This means that if a user has set their computer up to give the best font and colour options for them, our site will follow these instructions. A text only version is available to make the site accessible to students using a screen reader, and the downloadable documents are available as word documents so that font colour and size can be changed before printing if necessary. The site and associated materials have been designed in accordance with the British Dyslexia Association ’s guidance, which turned out to provide a good visual feel for all students.

Details of the project

Initial outreach&Schools project

The eMalaria system was used in a number of schools in the region and supported by visits by the team. The project was also supported by workshops and talks delivered by project team members at the request of participating schools. The general format of these consisted of a 45-minute talk covering drug design methodology and how the project follows these principles, followed by a 45 minute session where students were given a compound to use as a lead for modification. Students then tried to find modifications to this molecule that would lead to better docking scores. The visualization of molecular shape was highly productive in supporting chemical education and the drug challenge taken up actively by many of the students; some interesting molecules resulted. We deployed the system for a number of University Open Days with perhaps the youngest participant being about 6 years old; this group designed molecules that came close to breaking the system!