Samuel William Canner
swcanner.bsky.social
Samuel William Canner
@swcanner.bsky.social
Part time PhD Candidate, part time freelance photographer, full time ultrarunner
Congrats!!!!
November 7, 2025 at 12:09 AM
In sum, we present the first de novo benchmark of protein-carbohydrate using AF3 and similar methods to identify the protein-sugar interactome at a structural level!

Once again, would like to thank my coauthors, who were integral to every step!
September 8, 2025 at 5:12 PM
Although our work shows the impressive capabilities of these models; our work is limited in that we have few structures in our set, and those structures are mostly globular single-domain proteins bound to short carbohydrates - similar to our work on CAPSIF.
September 8, 2025 at 5:10 PM
Previously, in PiCAP we uncovered the protein-sugar interactome, identifying over 7.5k human proteins that likely bind to carbohydrates. Since AF3 and other methods do well 85% of the time - can we use AF3 to predict these structures? Simple answer: No, not just yet on a high throughput scale
September 8, 2025 at 5:06 PM
But, can these models tell us when they don't perform well - using their confidence metrics like ipTM or pLDDT? The simple answer - kinda. AF3 is incredibly overconfident, but there is a moderate trend in most models from prediction confidence and prediction accuracy.
September 8, 2025 at 5:03 PM
Across the board, all models perform great at protein-carbohydrate docking, achieving 85% of top-5 structures with at least acceptable quality! However, the largest limitation is that overall performance decreases as saccharide length increases.
September 8, 2025 at 4:59 PM
In this work, we developed a unique test set of 20 proteins to evaluate the performance of AF3, Boltz-1, Chai-1, DiffDock, and RFAA at protein-carbohydrate docking. We additionally made a new metric: DockQC, inspired by protein-protein docking to evaluate their performances across many test cases!
September 8, 2025 at 4:57 PM
I’d like to thank my PI Dr @jeffreyjgray.bsky.social
and co-mentor Dr. Ronald L Schnaar for their advise on this project. I’d also like to thank Sergey Lyskov for implementing the ROSIE server!
March 17, 2025 at 7:05 PM
I would also like to thank the @rosettacommons.bsky.social at large, especially Yijie Luo for providing us with their designed carbohydrate non-binder dataset (which they used to train their CLIMBS algorithm, also just published on BioRxiv!).
March 17, 2025 at 6:02 PM
If you’d like to use CAPSIF2 or PiCAP, you can do so freely at our github link: github.com/Graylab/picap or you can use our server on ROSIE: r2.graylab.jhu.edu/apps/ !
March 17, 2025 at 6:00 PM
We also provide an updated model of our CAPSIF, a model for predicting carbohydrate binding regions of proteins. Comparing CAPSIF2 with @parthbibekar.bsky.social’s PeSTo-Carbs, finding their model outperforms CAPSIF2 on the TS90 dataset, but, CAPSIF2 modestly outperforms P-C on a larger dataset.
March 17, 2025 at 5:59 PM
Now that the stage is set: what proteins bind to carbohydrates? We used PiCAP on three proteomes: E. Coli, mice, and humans and found that PiCAP predicts 35-40% of proteins bind to carbohydrates. And we provide a table of all proteins and their predictions for open scientific use and validation!
March 17, 2025 at 5:56 PM
PiCAP does well on the test set -- but how does it do on other datasets that aren’t manually sculpted? We compare PiCAP to LectomeXplore finding a 99.5% agreement between the methods. We also interrogated the ganglioside interactome finding that PiCAP has a strong correlation with the experiments!
March 17, 2025 at 5:54 PM
To do this we developed a deep learning (DL) model named Protein interaction of CArbohydrate Predictor (PiCAP). We find that PiCAP has approximately a 90% accuracy on identifying carbohydrate binding proteins, with limitations primarily on proteins that have reduced evolutionarily evidence (Abs).
March 17, 2025 at 5:52 PM
It all started by asking just a simple question: “What proteins bind carbohydrates?” Lectins bind carbs, but, there are myriads of other proteins that bind carbohydrates (e.g. RTKs). And so we set out to find that out: can we find all the proteins in the human proteome that bind carbohydrates.
March 17, 2025 at 5:51 PM