I have been rather quiet here, my personal blog for a variety of reasons, mainly because past collaborations encroaching into the spare after-hours I would otherwise dedicate to it (i.e. weekend early mornings). I have been involved in various projects, many of which I would like to write blog post about or people would like me to write about, so I am well behind on what I would like to post. However, as part of OPIG, I have written a few posts there (Blopig), some on requests (who would willingly write about fixing CUDA installations or exposing Jupyter notebooks in a compute node via reverse port forwarding?) and some out of personal choice.
As of February 2024, these are the comp chem/biochem ones:
- The workings of Fragmenstein’s RDKit neighbour-aware minimisation
- Demystifying the thermodynamics of ligand binding
- Placeholder compounds: distraction vs. accuracy
- Customising MCS mapping in RDKit
I have a few upcoming posts I am slowly writing, namely about
- Escape from Flatland, and into Cthulhu's realm
- Compound picking: balancing predicted affinity, risk, and cost while sampling novel interactions at the Pareto frontier
- Primer on pathogenic protein variants beyond simple destabilisation
- Programmatically working with XChem data and the multilayered nature of non-binders
- Cranking up the amount of Rosetta analyses in RFdiffusion
If you'd like a sneak-peak feel free to email me at matteo.ferla (gmail or stats.ox.ac.uk). I get one or two out-of-the-blue emails a week and I do tend to reply to them.
Lastly, I ought to mention that I started posting my coding-problem solutions as comments in a Gist, so if you, like someone who emailed me the other day, found a coding solution of mine but could not find it again try there!
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