Monthly Archives: April 2020

HERO proteins are here to save you (assuming you’re another protein or a fruit fly)

For one of OPIG’s short talks, I recently introduced the work done by Kotaro Tsuboyama et al. found in the paper A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. As the name implies, HERO proteins have been found to retain function even after being boiled at 95C and have been found both in Drosophila and human HEK293T cell lines. Whilst it’s not impossible to find proteins which can “survive” 90+ Celsius, these are expected to be the reserve of extremophiles, not found in humans or fruit flies.

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Don’t drink bleach, don’t share canards!

Beyond the thousands of deaths and the millions of infected people, the COVID-19 pandemic has quickly transformed Western society. This virus has provoked the confinement of millions of people in their houses, the closure of bars, restaurants, and pubs, schools, museums, and theatres. However, for this post, I will focus on another side effect of the pandemic: the spread of canards, which flow even faster than the virus itself.

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Non-specialist intro: Convalescent sera and some thoughts on its relevance to structural biology

A couple of weeks ago, I gave a group meeting talk on my current research. Interestingly most of the questions I received were not directly related to my research methods, but rather, on the broader application of antibody-related therapies, as I used the example of convalescent sera as a potential ‘quick fix’ in the current COVID-19 pandemic, to motivate why antibody research is important! So I thought in this blog post, I would give a quick introduction to convalescent sera. (Disclaimer: This does not contain any clinical information.)

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Understanding the synthesizability of molecules proposed by generative models

De novo molecular design is a computational technique to generate molecules with desired properties from scratch. Classical generative algorithms are based on Genetic Algorithms (GA) and the iterative construction of molecules from molecular fragments. Recently, Variational Auto-Encoders (VAEs), Generative Adversarial Networks (GANs) have been developed for this task, however, the synthesizability of the proposed molecular structures remains an issue. Gao and Coley[1] provided an analysis of the synthesizability of the molecules proposed by these de novo generative algorithms, and discuss their strengths and weaknesses.

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GEMMI: A Python Cookbook

General MacroMocelecular I/O, or GEMMI, is a C++ 11 header only library for low level crystalographic .

Because its header only it is certainly the easiest to access and use low level crystalographic C++ library, however GEMMI comes with python binding via Pybind11, making it arguably the easiest low level crystalographic library to access and use in python as well!

What follows is a cookbook of useful Python code that uses GEMMI to accomplish macromolecular crystalographic tasks.

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