Ghoulish calculations? Sounds like a job for an RTX6666
Matteo Ferla
@matteoferla.bsky.social
Cheminformatician/computational-biochemist working on drug discovery (señor postdoc, CMD-PX / OPIG, University of Oxford) ⌬ ⚗️💻 Author of michelanglo.sgc.ox.ac.uk and Fragmenstein
I wrote a blogpost ( blog.matteoferla.com/2025/08/conf... ) about a potential aid to crystallography thought up when I worked w/ @xchem.bsky.social: generating a fake crystal lattice from a protein model in order to design optimal crystal contacts with ProteinMPNN. #ProteinDesign #StructuralBiology
Confabulating a crystal lattice
Matteo Ferla, a blog containing various tidbits of useful information, how-tos and what-ifs from biochemistry to Star Trek.
blog.matteoferla.com
As my final task working in @opig.stats.ox.ac.uk & @cmd.ox.ac.uk I wrote a code-filled blogpost discussing what I did as a poweruser with RFdiffusion & co. to design inserts, linkers and more for specific problems to aid crystallography: www.blopig.com/blog/2025/04... 📚 #proteinengineering
AI generated linkers™: a tutorial | Oxford Protein Informatics Group
blopig.com
Some ideas are cool, but aren't easily doable, so I wrote a blog post about one: de novo binders that spontaneously form an irreversible isopeptide bond with their target protein www.blopig.com/blog/2025/01... —what's the catch? Many
OPIG is now on Bluesky! Follow us for updates about the group's latest work, web app updates, and more. opig.stats.ox.ac.uk
OPIG
Oxford Protein Informatics Group
opig.stats.ox.ac.uk
Fragmenstein is finally published! ⌬🔩📗 This tool stitches together the atoms of parent hits and re-animates (minimises) them into a conformation close to the parents, preserving their interactions: a must for crystallography-driven drug discovery doi.org/10.1186/s133... #chemsky #drugdiscovery
Fragmenstein: predicting protein–ligand structures of compounds derived from known crystallographic fragment hits using a strict conserved-binding–based methodology - Journal of Cheminformatics
Current strategies centred on either merging or linking initial hits from fragment-based drug design (FBDD) crystallographic screens generally do not fully leaverage 3D structural information. We show...
doi.org
There has been great discussions here about natural products for drug discovery. I want to add my take: the biosynthesis of these compounds often evolved as deterrents to kill us while our physiology evolved to fight them. blog.matteoferla.com/2025/01/natu... #chembio #chemsky
In an internal presentation today I had this comedy slide, which I am rather pleased with
