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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

Phil Hinchliffe and Steve Burston, Delhi Kalwan, Jennifer de Jong, Fabio Parmeggiani and Paul Race

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

This project was made possible thanks to a collaboration between @bristoluni.bsky.social and @ebi.embl.org. A great thanks goes to @robbarringer.bsky.social, Ioannis Riziotis (Crick), Antonina Andreeva, @alexbateman1.bsky.social and ...

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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 · 20/03/2025

🙏 Special thanks to my amazing collaborators: Ioannis Riziotis, @robbarringer.bsky.social, Antonina Andreeva and to my supervisor @alexbateman1.bsky.social for their invaluable contributions to this work!

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Francesco Costa @atsocf.bsky.social · 20/03/2025

💻 Available as a Python package for easy integration into bioinformatics workflows, and accessible via Google Colab for everyone: colab.research.google.com/github/Franc...

colab.research.google.com

Google Colab

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Francesco Costa @atsocf.bsky.social · 20/03/2025

🧬 Isopeptor enables reliable detection and geometry evaluation of these covalent links using a template-based strategy powered by pyJess. 🔍 The tool demonstrates a precision of 1.0 and recall of 0.947 in identifying incorrectly modelled isopeptide bonds in PDB structures.

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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

A special thanks goes to my supervisor @alexbateman1.bsky.social and to @matthiasblum.bsky.social for their support and guidance. 7/7

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

Our findings have important implications for improving structure predictions, especially for proteins from organisms with limited representation in sequence databases or for rapidly evolving taxa. 6/7

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

We show that using high plDDT models as templates can increase the speed of AlphaFold2 as implemented in ColabFold, potentially reducing computational costs and carbon footprint. 5/7

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

We introduced a novel "Best Pick" strategy that combines predictions made with and without multiple sequence alignment (MSA) information, selecting the model with the highest average plDDT. 4/7

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

This observation led us to explore whether low-confidence predictions could be improved using high-confidence templates from the same protein family. About one-third of low-confidence structures can be "rescued" to reasonable confidence levels using this method. 3/7

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

By observing the plDDT distribution within protein domain families, we noticed a certain degree of heterogeneity in the confidence of AlphaFold2 predictions. 2/7

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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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