GlycoShape
LightNews LightNews
banner
glycoshape.org
GlycoShape
@glycoshape.org
140 followers 150 following 98 posts
Glycan 3D database and toolbox for the reconstruction of glycoproteins from the RCSB PDB and EMBL-EBI AlphaFold repositories or own. Find us at https://glycoshape.org. Curated by head chef @elisafadda.bsky.social and sous chef @ojas-singh.bsky.social
Posts Replies Media Videos
glycoshape.org
Phenomenal #glycotime by Meg Lunn-Halbert, Joel Allen and colleagues demonstrates through de novo protein design how steric hindrance controls N-glycan maturation ⬇️

doi.org/10.64898/202...

Protein design with RFdiffusionAA coupled with glycosylation with GlycoShape 🧪
screenshot of Fig. 2 in the paper, titled "Systematically altering steric restriction controls glycan processing" the following corresponds to the figure caption in the paper. Panel a, AF3-predicted protein with GlycoShape-modeled Man9 glycan (green) for glycoproteins THRgly1-4. b-d, Deconvoluted intact mass spectra for analyzing native glycosylation with 1–3 major peaks corresponding to glycosylation shifts labeled. Glycans matching in theoretical molecular weight to the corresponding shift are schematically annotated as follows: mannose residues as green circles, N-acetyl glucosamine residues as blue squares, galactose as yellow circles, sialic acid as pink diamonds, and glucose as blue circles. Unglycosylated sizes are estimated based on predicted MW and labeled, when present. b: Native glycosylation. c: Native protein digested with Endo H. d: Overlaid protein from kifunensine-treated cells (color, solid line) and digested with Endo H (gray, dotted line). Estimated predominant glycans present are shown in MW (Da) differences from predicted unglycosylated size. For peak table see Supplementary Data S3; amino acid sequences provided in Supplementary Data S1.
October 9, 2026 at 8:52 AM
glycoshape.org
Refreshed ReGlyco Filter in bioRxiv 🧪(doi.org/10.64898/202...) in view of the upcoming Protein Design Competition on Monday 28/09 🎉🔥

proteinbase.com/competitions...

Each week a new target and if it's a glycoprotein, glycoshape.org and ReGlyco Filter can help screen and optimise your binder design
NiV G was the target of the Adaptyv Bio Protein Design Competition 2025. Structure of the Nipah Virus Glycoprotein (NiV-G) homotetramer (aa 92-602) reconstructed from cryo-EM structures (PDB 7TXZ and 7TY0) bound to broadly neutralising antibody nAH1.3 Fabs(Wang et al. 2022) (not shown). Static (single) glycans 3D structures (shown with sticks in blue) were reconstructed with GlycoShape ReGlyco(Ives et al. 2024). The glycoform selection was guided by glycoproteomics analysis(Hawkins et al. 2025). The visible six glycan sites on chains A, B and D are mapped onto the structure, while glycans on chain C are not labelled for clarity
September 25, 2026 at 6:17 PM
Reposted by GlycoShape
elisafadda.bsky.social
Fantastic opportunity to talk, listen and discuss the future of #glycotime 🧪 with ECRs and PhD students at the upcoming GRS Glycobiology 2027 organised by the über talented
@j-a-n-alexander.bsky.social and @lornamilne.bsky.social who put together a sensational programme. Register asap!! ⬇️
GRS flyer with a view of the town of Ventura (CA) from the hills, tree on the right hand side, sea in the distance. Flyer has a blue background
September 16, 2026 at 3:52 PM
Reposted by GlycoShape
elisafadda.bsky.social
🚨 Want to be part of top #glycotime on the seaside in the California sunshine? Register to the 2027 GRC Glycobiology ⬇️ Stacy and Lance put togteher up one of the most exciting programmes I have ever seen with phenomenal keynotes!

We have 32 abstracts to select, so the next speaker could be YOU! 😎
Announcement of the GRC Glycobiology 2027 to be held in Ventura CA on March 14 to 19, 2027. Blue background with an photo of Ventura from the visitventuraca.com
September 14, 2026 at 5:26 PM
glycoshape.org
🚨 New version of GlycoShape is now live at glycoshape.org 🥳 Powered by crabWURCS everything runs on your browser and while you save all you ReGlyco work and go back to it whenever you like 😎
Among other new things: new slick drawer, much easier to use, new slick SNFG representations and new layout
screenshot to represent the new layout of GlycoShape, here the database screen added NEW sticker
September 4, 2026 at 5:33 AM
Reposted by GlycoShape
elisafadda.bsky.social
I will be in Geneva at #ECCB2026 for a super #glycotime workshop in glyco-bioinformatics hosted by @glycoexpasy.bsky.social to present a hands-on guide to the new layout and features of @glycoshape.org

If you want to hear all about it, just sign up! ⬇️

eccb2026.org/communities-... online and free
screenshot of the title slide of my talk showing a graphical representation of a cell surface in brown with glycans added dfrom structures in Glycoshape. the title of the talk reads 3D glyco-bioinformatics with GlycoShape
September 2, 2026 at 1:54 PM
Reposted by GlycoShape
nmriley.bsky.social
We then took a deeper dive into our EpCAM data to look at what integrating bottom-up glycopeptide and intact glycoproteoform measurements can get us, and @emmajays.bsky.social helped us use @glycoshape.org to model how a glycoproteoform with two occupied N-glycosites might look like.
August 28, 2026 at 3:16 PM
glycoshape.org
Want to know more about #glycotime resources in bioinformatics and/or build some glycoproteins with GlycoShape? Join us online on Sept 4th for fabulous hands-ON workshops organised by @glycoexpasy.bsky.social 😎🥳🧪

Online registration is FREE (Price: 0 CHF) here, eccb2026.org/communities-...
glycoexpasy.bsky.social glycoexpasy.bsky.social @glycoexpasy.bsky.social · Aug 11
Attending @eccb-europe.bsky.social in Geneva this year? Then, you can join our workshop! Programme and registration is here: eccb2026.org/communities-...
it's free 🙂 but hurry!
August 28, 2026 at 11:08 AM
glycoshape.org
⬇️ #glycotime 🧪
elisafadda.bsky.social Elisa Fadda @elisafadda.bsky.social · Jul 17
Isn't it amazing when a fresh new preprint is out on Friday? 😎🥳 Check out the fabulous work by @beatricetropea.bsky.social who gives us a clear mechanistic explanation behind the 'peculiar' structure of the LLO donor preferentially chosen by eukaryotic OST 🤓😍

doi.org/10.64898/202...
Figure 1. Structural overview of the yeast OST complex and donor-binding site. (a) 3D structure of the yeast OST complex embedded in the ER membrane (brown sticks), showing the 8 subunits as surface color coded according to the labels. The lipid-linked oligosaccharide (LLO) donor is shown in orange and the backbone of the acceptor peptide is shown with a cartoon representation in yellow. The central panel shows the 2D SNFG representation of the LLO donor, with labels specifying glycosidic linkages and the nomenclature used for the branches. Below we show the sequence of an acceptor peptide, i.e. YJR1_N99, used as substrate in all MD simulations in this work, where the target asparagine was previously characterised as efficiently glycosylated(Khaleque et al. 2025). (b) Close-up view of the donor-binding pocket from the cryo-EM structure (PDB ID: 8AGC), showing the resolved LLO donor represented in sticks (orange) and SNFG symbols and the Stt3 N539 glycan (white). (c) Close-up view of the donor-binding pocket from the 3D model used in the MD simulations with the reconstructed N-glycans. The monosaccharides resolved in the cryo-EM structure are shown in white and orange as in panel b, whereas the monosaccharides added in the reconstruction of the full LLO donor and N539 glycan are highlighted in dark orange and grey, respectively. Rendering with Visual Molecular Dynamics (Humphrey, Dalke and Schulten 1996) (VMD) (https://www.ks.uiuc.edu/Research/vmd/).
July 17, 2026 at 1:43 PM
glycoshape.org
The fully glucosylated LLO structure is the preferred substrate of eukaryotic OST, especially engineered to enhance N-glycosylation efficiency; but how does that work? and why do we need all those glucoses?

@beatricetropea.bsky.social answers all these Q in a new preprint ⬇️

doi.org/10.64898/202...
How the terminal glucoside of the N-glycan donor affects the catalytic efficiency of the eukaryotic oligosaccharyltransferase
The eukaryotic oligosaccharyltransferase (OST) is the enzyme responsible for initiating N-glycosylation of secreted proteins by transferring a pre-assembled lipid-linked oligosaccharide (LLO) donor to...
doi.org
July 17, 2026 at 12:54 PM
Reposted by GlycoShape
elisafadda.bsky.social
As a fun educational/inspirational #glycotime we decided to curate a Blog on glycoshape.org, you can find it under Resources or here glycoshape.org/blog

You can *sign up* to get an email when we post a new entry

The latest is E04:Let's talk about glycan binding to viral (glyco)proteins 🧪
Figure 1: Left. Structure of the SARS-CoV-2 S (gamma strain ectodomain; PDB 7sbs). Chains are represented in different colours, pink for chain A, grey for chain B and green for chain C, also in the legend at the bottom left corner. Right. Structure of an isolated RBD (grey surface) from the MD trajectory in complex with a GM1 oligosaccharide (C atoms in purple, O in red). The N345 glycan is not shown for clarity. The structures of the GM1 and GM2 oligosaccharides are shown below the RBD structure with SNFG symbols.
July 2, 2026 at 4:37 PM
glycoshape.org
Un-crystallisable glyco-complexes anyone?

New work led by John Klassen's lab introduces antibody masking-native mass spectrometry (AM-nMS) a spatially resolved assay that allowed us to map glycan binding sites across the SARS-CoV-2 RBD. The results match our MDs! 😜

All details glycoshape.org/blog
screenshot of the E04 new blog entry on https://glycoshape.org/blog titled Let's talk about glycan binding to viral (glyco)proteins
June 30, 2026 at 5:15 PM
glycoshape.org
glycoshape.org has now a blog where we discuss (yep you got it) glycans, glycoproteins and fun stuff!

Season 1 is out with:

Ep01: Why should we care about glycan heterogeneity?
Ep02: How can we include glycan heterogeneity in a 3D framework?
Ep03: Molecular precision glycoscience: Enter Siglecs
Header of the Blog page on https://glycoshape.org/blog that you can find in the drop-down menu under Resources> Blog
June 19, 2026 at 4:34 PM
glycoshape.org
Next time you hear 'glycans are just a fancy protein decoration' 😱 show them this fabulous work led by Katrine Schjoldager and team at the CGR 🇩🇰 with us 🇬🇧 showing how

The ligand preference of LRP1 is regulated by O-glycans

Out now www.science.org/doi/10.1126/...

🧵1/10 ⬇️
The ligand preference of LRP1 is regulated by O-glycans
GALNT11-mediated O-glycans modulate LRP1 uptake of tau and Aβ, unveiling glycan-driven mechanisms in neurodegenerative pathways.
www.science.org
June 9, 2026 at 4:39 PM
glycoshape.org
Glycoheterogeneity is an aspects of glycobiology that most would class into a category between difficult and intolerable, but @benschulz.bsky.social and us love it! So we wrote a whole review in Current Opinion in Structural Biology on it

🧵1/8 ⬇️

doi.org/10.1016/j.sb...
screenshot of the the title of the review "Heterogeneity of glycoproteins: Why does it matter and how to account for it"
June 5, 2026 at 5:57 AM
Reposted by GlycoShape
elisafadda.bsky.social
🚨 #glycotime seminar alert! June 22nd, 2026 4pm JST (8am BST) @kiyokof.bsky.social will present the GlyTouCan v.4 in the next GlySpace Alliance Seminar event 🔥

If you use @glycoshape.org, you know already aboutGlyTouCan IDs. Tune in ⬇️ to discover what GlyTouCan can do for your research 🥳
June 3, 2026 at 4:48 PM
glycoshape.org
Carbohydrate-binding is a small profit affair, so proteins often adopt complex multidomain architectures enabling a mechanism known as 'binding cooperativity', where binding to one monomer contributes to the binding affinity of the whole systems

BUT how does it actually work?

🔥 #glycotime 🧵1/4 ⬇️
Alexis Rose: I Don't Know You Tell Me (Schitt's Creek)
ALT: Alexis Rose: I Don't Know You Tell Me (Schitt's Creek)
static.klipy.com
June 2, 2026 at 5:34 PM
Reposted by GlycoShape
elisafadda.bsky.social
A fab, sunshiny week in 🇩🇰! Great #glycotime 🧪 at the CBM16 in Helsingør, with posters
Bea: regulation of N-glycosylation by OST (doi.org/10.1101/2025...)
Silvia: Siglec-6 high-recision recognition of glycolipids (doi.org/10.1038/s420...)
Ojas: de novo binders design (doi.org/10.64898/202...)

🧵⬇️
From the left, Elisa, Ojas, Bea and Silvia. Blue skies above Helsingor, Denmark for the CMB16 Silvia (left) introducing her work on Siglec 6 (https://doi.org/10.1038/s42003-026-09609-8) in a flash talk at CBM16 Elisa (small with red jumper in the left corner) presenting GlycoShape in her "work along" part of the talk, with people in the audience rebuilding the glycosylation of IL5 on GlycoShape ReGlyco
May 7, 2026 at 4:43 PM
glycoshape.org
Daily job count is quite high these days after the release of our case study 1 week ago and of the ReGlyco de novo Binder Design Filter notebook ⬇️

doi.org/10.64898/202... and res. therein

So exciting to see a growing number of researcher including glycosylation in their studies! 🎉 #glycotime 🧪
Bar graph showing the GlycoShape job count x day in April 2026
April 24, 2026 at 2:56 PM
glycoshape.org
We are proud to be part of @elixiruknode.org as the @unisouthampton.bsky.social node, and to share our expertise in structural and computational glycoscience 🧪, together with our OA resources thought it. Check out the announcement below for more information ⬇️ 🥳
April 21, 2026 at 11:08 AM
glycoshape.org
Most biologics are glycosylated and some of them heavily. In this “fresh off the press" #glycotime preprint we look into how a filter that accounts for glycosylation explicitly in 3D can help reduce lab costs and increase the efficiency of de novo binder design pipelines. Short 🧵 ⬇️ 1/7
biorxivpreprint.bsky.social bioRxivpreprint @biorxivpreprint.bsky.social · Apr 17
Integrating glycosylation in de novo protein design with ReGlyco Binder Design Filter https://www.biorxiv.org/content/10.64898/2026.04.16.718906v1
April 17, 2026 at 11:21 AM
glycoshape.org
Super congratulations to the Siglec (and many other stories) extraordinaire Dr. D'Andrea!!! 👩‍🎓🎉🥂🍾

A huge thank you to the fantastic examiners Alba Silipo (external) and Trinidad Velasco-Torrijos (internal) for your expert and in-depth examination, which made Silvia's viva a great day to remember 😎
From left: Prof Alba Silipo (UniNa, Federico II), Elisa Fadda, Dr Silvia D'Andrea, and Dr Trinidad Velasco-Torrijos, yellow table and amazing red velvet cake
March 30, 2026 at 1:33 PM
glycoshape.org
Super congratulation to Dr Akash Satheesan from the glycoShape team, who graduated officially today with a PhD @maynoothuniversity.ie !! 😎🎓👏🥳🥂

The 🔺-red gown definitely suits you well Akash! 😍
PhD graduation photo of Dr Akash Satheesan. From the left Beatrice Tropea, Akash (showing his well deserved parchment), Ojas Singh and Silvia D'Andrea
March 19, 2026 at 5:23 PM
glycoshape.org
Lectins are known to be low affinity binders with relatively broad glycan target preference. In this work live in @commsbio.nature.com we show how Siglecs change this paradigm, acting as molecular precision tools required to fine tune immune response 🤯 #glycotime 🧵⬇️

doi.org/10.1038/s420...
Glycolipid recognition and binding by Siglec-6 hinges on interactions with the cell membrane - Communications Biology
Siglecs are immunoregulatory lectins with very similar architectures. The authors show how the V-set domain of Siglec-6 allows it to select for precise sialylation patterns in specific biological envi...
doi.org
March 2, 2026 at 5:27 PM