PDBe is at #ISMBECCB2025!

Structural Bioinformaticians & Computational Biologist sharing insight & inc. research on:

...GWAS (Genome-Wide Association Studies) + AlphaFoldDB & PDB + plants...
📖 doi.org/10.1016/j.cs...

Abstracts:
🔗 www.iscb.org/ismbeccb2025...

@iscb.bsky.social @3dsig.bsky.social

📣 Working with AlphaFold's PAE? The latest instalment in our 'Protein Model Quality' series may be of help! Find out how you can visualise the metric with your alignments and 3D structures in Jalview.

▶️ Watch the new training video here: www.youtube.com/watch?v=jowU...

Accessing a wealth of structure data to integrate with your #MSA is possible accessing the #3DBeacons network through #Jalview.

Get experimentally determined structures from @pdbeurope.bsky.social as well as predicted structure models from #AlphaFoldDB, @swiss-model.bsky.social and other providers!

Ivanna Pidruchna is the UX/UI Expert in the AlphaFoldDB team. Her work focuses on guiding our website updates at AlphaFold DB and PDBe to ensure the best possible experience for our users.
#IWD2025 #WomenInTech #WomenInScience

On this International Women’s ♀️ Day, we celebrate the diverse talented women who support #structuralbiology resources, such as:
🧪 PDBe & AlphaFoldDB
🧪 EMDB
🧪 EMPIAR

Leaders & more... Let's meet some of them!
🧵 (1 of 16)

#InternationalWomensDay #WomenInTech #WomenInScience

nice #Alphafoldology update of domains additions to AlphafoldDB

I generally use both EBI and NCBI because while they overlap for much of the core data, they each have strengths. E.g EBI manage the alphafoldDB

Ivanna Pidruchna is the UX/UI Expert in the AlphaFoldDB team. Her work focuses on guiding our website updates at AlphaFold DB and PDBe to ensure the best possible experience for our users.
#IDWGS #WomeninSTEM #WomenInScience

This week we had International Day of Women and Girls in Science 👩‍🔬 🥼 🔬

There are many women working to provided the resources at PDBe, AlphaFoldDB, EMDB and EMPIAR. Lets met a few of them!

#IDWGS #WomeninSTEM #WomenInScience #WhatAScientistLooksLike

The SwissProt subset of AlphaFoldDB (540k proteins) takes even less: under 2 hours (proteins are smaller on average).

But does prediction speed matter? 🤔 It depends. In most cases, probably not. After all, if you have only a few structures, it’s worth waiting for more accurate predictions.

(2/n)

TMVisDB: Annotation and 3D-visualization of transmembrane proteins [updated]
Enables browsing & 3D visualization of 46M predicted transmembrane proteins, combining AlphaFoldDB structures with topology annotations.

Try out our integration of the amazing protein structure search tool #Foldseek on #SubtiWiki (subtiwiki.uni-goettingen.de/foldseek)! Just upload a structure or use PDB/AlphaFoldDB entries to find similar structures. #IMPRS-GS #UniGoettingen
#alphafold #bacillus #subtilis

We combine the strengths of different datasets and try to mitigate their weaknesses. We pretrain on a processed AlphaFoldDB, incentivizing to sample diverse structures. Then we finetune on loads of MD simulation data and experimental protein stabilities.

🤔

"Chai-1 is trained on both PDB and AlphafoldDB" #alphafold

The LAYN:p extra exon (in red) just adds a bit of length to an nward IDR in the AlphaFoldDB structure model.

Passionate about biology and data engineering? We are currently seeking a Data Engineer who will work with optimizing our data pipelines and ensure the continued sustainability of our PDBe, PDBe-KB & AlphaFoldDB services! Apply by 12 May 2024: embl.org/jobs/positio...

We’re delighted to have joined BlueSky to engage with the scientific community about macromolecular structures and related data. Follow us for updates on PDB and #AlphaFold DB databases, more info on our resources such as #PDBeKB, and for lots of beautiful structure images!

Our Foldtree notebook allows you to compute and visualize trees from protein structures in the browser. Generate trees from either 1) a set of protein structures, 2) AlphaFold​DB identifiers or 3) an #AlphaFold cluster identifier cluster.foldseek.com.
🌐 colab.research.google.com/github/Dessi...

So I decided to do this... instead of searching alphafold models against the PDB (as would online DALI). I flipped it and searched models against the entire AlphaFoldDB. One could also merge all structures (AlphaFold & PDB) for a giant non-redudant DB....