Monday, 19 March 2018

The curious case of fluorescein and implicit waters

I recently was asked a straightforward task: get the energy scores of a given protein by itself, conjugated with fluorescein maleimide and its ring opened form. Despite that I failed miserably because of implicit waters playing odd tricks.
Given that it is of no real use, I am happy to share so to give a tutorial of how to do that in Rosetta (ligand docking), which I found taxing the first time.

Saturday, 6 January 2018

Skewed mutational biases: English scrabble with Klingon tiles

Skewed mutational biases: English scrabble with Klingon tiles

Random set of 7 TlhIngan Hol tiles
In a game of Scrabble one draws seven tiles from a bag and the best results are found when a bag and the language used match. In library making with error-prone PCR one does not have that luxury, but different methods differing degrees of fairness. Mutazyme is like playing in English with a Latin tile set, while manganese Taq with equal nucleotides is like playing in English with a Klingon tile set.

Thursday, 4 January 2018

Pi projects: a new year's resolutions

2018 is here. I have papers that I want to or have to write and endless tasks I want to complete, but life is not all about career-driven self-sacrifice, it is also about having fun and what better way than with physical computing. And more time passes the more Rasberry pi projects I find I want to do. So I thought I'd share my shortlist of what I think are the most useful.