The Blog is a collection of News, Blog posts, technical tips and tricks and other writings from my sphere of interest.
- Esben Jannik Bjerrum


Congratulations to Khanhvi Tran

cand.pharm Khanhvi Phuc Tran

cand.pharm Khanhvi Phuc Tran

Yesterday I was the external examiner at Khanhvi Tran’s Master thesis defense. She had been working on upgrading the SmartCYP program from version 2.4 to 3.0, together with her supervisors Associate Professor Lars Olsen, Ph.D student Marco Montefiori  and Professor Flemming Steen Jørgensen.

The program predicts site of metabolism (SOM) on small molecules for the Cytochrome P450  subtypes 34A, 2D6 and 2C9. It uses a fragment library with precomputed DFT energies as well as accessibility features (Relative Span and 2DSASA) to give fast predictions of SOMs.
Khanhvi gave a nice presentation about the background and undertakings of her project with interesting scientific discussions afterwards.
A big endeavor was the translation/rewriting of the program from Java into Python to pave the way for more easy extensions, where she did a huge work translating the SMARTS fragment matching rules  developed for the CDK toolkit  into SMARTS that worked with RDKit. Subtle differences in the atom typing and aromaticity model between the two toolkits made this a non trivial task. Additionally, the fragment library was extended with new rules using Quantum Mechanical DFT calculations, leading to improvements in predictions.
The program will be available with a new and improved web interface as soon as the Faculty IT department has made the server ready.

Congratulations once again with your Masters degree, Khanvi. I wish you good luck and I’m sure that you will find a job where you can combine your pharmaceutical sciences degree with your interest and skills in programming.

Best Regards
Esben Jannik Bjerrum

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