Fragment-based drug discovery (FBDD) is based on the idea that using small (< 300 Da), highly soluble compounds to screen against a target will give higher hit rates and sample chemical space more efficiently compared to screens using larger, drug-like compounds.
Category Archives: X-ray Crystallography
Real Space Correlation Coefficient
Introduction
In crystalography we are often faced with the question of how well a part of our model fits the data. Now crystalography has well developed probability models for the reflection amplitudes given then entire fitted model, but these do not provide a metric for “how much of the ligand is inside the blob”. This is because the reflection based models are inherently global.
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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.
Continue readingCoronavirus
A zoonosis is an infectious disease that has jumped from a non-human animal to humans.
The coronavirus disease 2019 (COVID-19) is one such zoonosis, and is caused by severe acute respiratory syndrome coronavirus 2 (SARS coronavirus 2, SARS-CoV-2, or 2019-nCoV). This is very similar to the SARS virus that emerged in 2003. Its recent emergence has resulted in a WHO-declared public health emergency of international concern.
Continue readingHandling electron density in python for fun and profit
No-one ever observed a pdb file in nature. The experimental data we build our protein models from is not quite so nicely paramterised. The vast makority of models are fit into electron density maps, mostly produced from macromolecular crystalography or cryo-em.
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