Matteo Ferla

Confabulating a crystal lattice Matteo Ferla, a blog containing various tidbits of useful information, how-tos and what-ifs from biochemistry to Star Trek.

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

17.08.2025 18:01 — 👍 4    🔁 0    💬 0    📌 0

AI generated linkers™: a tutorial | Oxford Protein Informatics Group

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

29.04.2025 15:40 — 👍 2    🔁 0    💬 0    📌 0

Why use a polyglycine linker in 2025?!

20.02.2025 14:41 — 👍 3    🔁 0    💬 0    📌 0

de novo binder that forms an isopeptide bond

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

26.01.2025 12:50 — 👍 4    🔁 1    💬 0    📌 0

OPIG Oxford Protein Informatics Group

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

15.01.2025 13:53 — 👍 10    🔁 6    💬 0    📌 0

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...

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

14.01.2025 16:42 — 👍 4    🔁 3    💬 0    📌 0

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

08.01.2025 22:29 — 👍 2    🔁 0    💬 0    📌 0

In an internal presentation today I had this comedy slide, which I am rather pleased with

19.12.2024 10:49 — 👍 0    🔁 0    💬 0    📌 0