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Reposted by Francesco Costa

Rob Barringer @robbarringer.bsky.social · 22/11/2025

Overjoyed to finally have our isopeptide bond paper out! If you're interested in the types of proteins and organisms that use a cool intramolecular covalent bond, check it out: bit.ly/4od3ux8 Plenty of future SynBio/EngBio applications planned! Thanks to all involved (character limits suck).

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Francesco Costa @atsocf.bsky.social · 13/05/2025

⚠️⚠️⚠️Preprint alert⚠️⚠️⚠️ We mapped intramolecular isopeptide bonds across the AlphaFold database and found that they are widely distributed in microbial surface proteins, such as fibrillar adhesins or pilins, suggesting new targets for broad-spectrum antimicrobial strategies.

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Francesco Costa @atsocf.bsky.social · 18/02/2025

Check out this article about my research at @embl.org where I focus on protein modelling and on the study of fibrillar adhesins. Recently, we developed a method to detect isopeptide bonds, a key stabilizing feature in bacterial proteins. Thanks @oanastroe.bsky.social for putting this together!👇 👇 👇

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Reposted by Francesco Costa

EMBL-EBI @ebi.embl.org · 16/12/2024

Prediction confidence scores help #AlphaFold users gauge the reliability of protein structure predictions. 🖥️🧬 But things get more challenging for protein families. A new method helps improve low confidence predictions within protein families. academic.oup.com/bioinformati...

Protein structure prediction from the AlphaFold Database

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Francesco Costa @atsocf.bsky.social · 09/12/2024

Excited to announce our latest publication: “Keeping it in the family: Using protein family templates to rescue low confidence AlphaFold2 models” where we explore plDDT variability in #AF2 models of @pfamdb.bsky.social domains. doi.org/10.1093/bioa... 1/7

doi.org

Keeping it in the family: using protein family templates to rescue low confidence AlphaFold2 models

AbstractMotivation. High confidence structure prediction models have become available for nearly all protein sequences. More than 200 million AlphaFold2 mo

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