Protein Data Bank

🚀 Introducing the NEW PDBe-KB Ligand Search!

🔎 Search by name, ID, formula, SMILES or SMARTs or simply draw a structure to find exact or similar ligands in the PDB.

✨ Multiple ways to search, One intuitive interface!

Try it: pdbe.org/chem

How do pLDDT, ipTM, ipSAE, pDockQ2 and LIS fit together?

See how these metrics work together to assess confidence in an AlphaFold DB complex interface.

🎬 Watch the full tutorial: youtu.be/k4yBqddtPyQ

#AlphaFold #AlphaFoldDB

📢 New in PDBe-KB! Explore MD simulation annotations in ProtVista: residue exposure from MDposit and membrane interactions from MemProtMD.

PDBe and PDBe-KB pages also link to simulations in MDposit.

🔗 ebi.ac.uk/pdbe/pdbe-kb/p…

A predicted interaction may involve only a small region of a protein complex.
How can we identify confidence in that local interface when surrounding regions have high PAE?
Our tutorial uses PAE matrix to explain how LIS can help 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AlphaFoldDB

Same predicted complex, different confidence scores:

ipTM: 0.38
ipSAE: 0.75

Why can these metrics differ? Full breakdown 👇
youtu.be/k4yBqddtPyQ

#AlphaFold #AFDB