Tuesday, 18 September 2018

Python website on a shoestring budget, a tutorial

If you have a Python script you want to make into a website yet want to do it for a cheap as possible, it may seem like an impossible cause. But it isn't. Three options are possible:
  1. use a free service
  2. use a grant-based service
  3. run a server at home on a Raspberry Pi
Each have their merits, but the latter more so. Hence, why this tutorial is dedicated to showing you how to do it.

Everything you wanted to know about isopeptide bonds in Rosetta, but were too afraid to ask

Rosetta is great at predicting (with some accuracy) the energies of variant proteins, however, to make the most out of it with proteins with internal isopeptide bonds a few considerations are needed.

Saturday, 25 August 2018

PCR distribution

The distribution of mutations in an error prone library has been modelled in Sun (1995) based on the underlying principle of a PCR reaction. In the paper it is found that the distribution becomes more and more similar to a regular Possion and the two are virtually the same after 10 cycles. However, given that one most likely does not know what one's PCR efficiency is, using this formula may be dangerous. Whereas in reality getting a better estimate of the mean number of mutations may be more helpful.

Sunday, 12 August 2018

Protein dropcaps

To make a webpage stylish does not mean that it cannot be biochemically themed. In fact, to can have both thanks to protein dropcaps! using the protein alphabet made by Prof. Mark Howarth in Nature Structural and Molecular Biology in May 2015(available Here) in combination with a wee JS script I wrote you can be a stylish biochemist. The script along with documentation is available in my GitHub page: https://github.com/matteoferla/protein_alphabet_dropcaps.

Saturday, 4 August 2018

A fully suicidal enzyme follows a second order equation

That a fully suicidal enzyme follows a second order equation is a rather intuitive statement, but it is nice to have formal proof, which is as follows.

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.

Sunday, 18 March 2018

GFP is technically a suicide enzyme

GFP has an oxygen dependent maturation step to form its cofactor. Therefore, it could be farcically considered a suicide enzyme... It performs a reaction: it converts oxygen to peroxide —doing a single turnover.