iiinova — where your digital self keeps evolving

Reposted by Ojas Singh

GlycoShape @glycoshape.org · 04/09/2026

🚨 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

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Reposted by Ojas Singh

Elisa Fadda @elisafadda.bsky.social · 17/07/2026

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/).

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Elisa Fadda @elisafadda.bsky.social · 10/07/2026

Excellent #glycotime in Bratislava for the #ICS2026 great catching up with so many amazing colleagues and friends about science, @glycoshape.org and all the fun stuff! 🥳 We had a fabulous time 😎

From left Ulrika Westerlind, me, Lara Mahal, Mark von Itzstein, Rob Woods, Vared Padler-Karavani, Matt Macaulay, Oren Moskovitz

Pistachio (top) chocolate (bottom) ice-cream cone with a wafer

Me during my talk, poster with sponsors on the left, me waving my arms as usual, and slide behind me (photo credit Mark von Itzstein)

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 30/06/2026

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

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 19/06/2026

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

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 09/06/2026

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 ⬇️

science.org

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.

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 02/06/2026

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 ⬇️

static.klipy.com

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)

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GlycoShape @glycoshape.org · 05/06/2026

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"

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Elisa Fadda @elisafadda.bsky.social · 05/06/2026

Ben @benschulz.bsky.social , Ojas @ojas-singh.bsky.social and I have been pondering about heterogeneity a lot lately 🤔 In this COSB review we discuss the fruits of our pondering, discussions and readings, and we share our awe for the power and ingenuity of glycoheterogeneity in a 🧵 @glycoshape.org

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Ben Schulz @benschulz.bsky.social · 05/06/2026

Glycoproteins can be hard to understand because they're complex, heterogeneous, and flexible. Integrating MS glyco(proteo)mics, structural biology, and molecular dynamics simulation data can help! www.sciencedirect.com/science/arti... @elisafadda.bsky.social @ojas-singh.bsky.social #glycotime

sciencedirect.com

Heterogeneity of glycoproteins: Why does it matter and how to account for it

Glycosylation can be critical for determining the structure and functions of proteins, but it is often neglected, leading to significant knowledge gap…

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Reposted by Ojas Singh

Elisa Fadda @elisafadda.bsky.social · 07/05/2026

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

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 24/04/2026

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

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Reposted by Ojas Singh

ELIXIR-UK @elixiruknode.org · 21/04/2026

The University of Southampton has joined ELIXIR-UK 🎉 From open-access glycan databases to data stewardship, Southampton brings a wealth of expertise to the network. Read more: elixiruknode.org/news/2026/un... @elisafadda.bsky.social @glycoshape.org #openscience #bioinformatics #datastewardship

elixiruknode.org

University of Southampton joins ELIXIR-UK as it newest member

The University of Southampton has joined ELIXIR-UK, bringing expertise in computational biology, bioinformatics, clinical data, and data stewardship.

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 21/04/2026

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 ⬇️ 🥳

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Elisa Fadda @elisafadda.bsky.social · 17/04/2026

We have some fresh and cool #glycotime 🧪 on the impact of including glycosylation explicitly in de novo binder design. Filtering the results of a recent open competition for novel binders to the Nipah Virus Glycoptrotein (NiV-G) with ReGlyco improves the pipeline efficiency significantly ⬇️

a. 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 Fabs30 (not shown). Static (single) glycans 3D structures (shown with sticks in blue) were reconstructed with GlycoShape ReGlyco17, where the choice of the glycan type was guided by glycoproteomics analysis36. 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. b. Structure of the glycosylated NiV-G recostructured with GlycoShape ReGlyco Ensemble29 using 150 frames from the MD trajectories of each selected glycan. Rendering effect is obtained with a “long exposure” filter to reflect the glycan dynamics. Sterically constrained glycans and rigid regions of the saccharides can be identified by the darker blue colour. c. Structure of the glycosylated NiV-G as in panel b. but with each one of the 150 glycan frames shown in dark blue, to illustrate the potentially occluded volume of the NiV-G protein surface

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 17/04/2026

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

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 02/03/2026

Silvia's simulations showed that while all epitopes expose Sia for binding, Siglec-6 recognises and binds only GM1 because of a key interaction with the membrane through W127 and K126, which orientates the V-set domain to bind the Sia through Arg122 and the terminal Gal to the C-C' loop 😎

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 03/01/2026

Happy new year 2026 #glycotime! 🥳 We just introduced some useful options to Re-Glyco Ensemble. In the Advanced Settings you can now select a seed (positive integer) to reproduce structural ensemble of your favourite glycoforms such as the one below that you will see soon in an upcoming paper,

Structure of a protein (cyan/teal) rendered as surface with 50 frames representing the dynamic ensemble of the glycans (white surface and sticks) depicted at the three sites (N93, N99 and N104) indicated by the 2D SNFG symbols and corresponding GlyTouCan IDs. Graphic rendering with VMD

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 11/12/2025

Super interesting work from @carolynbertozzi.bskyverified.social group about the effects of glycosylation in protein structure and function at the proteome scale 🤯💥🤩 Results show that sialylation and fucosylation are crucial, which makes a lot of sense. We did some extra bits 🧐 with GlycoShape ⬇️🧵

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Reposted by Ojas Singh

GlycoShape @glycoshape.org · 05/12/2025

We just did some maintenance and updates to glycoshape.org, ✅ Fancy background with floating SNFG symbols 🤩 ✅ 'Latest Updates' feed from this account on bsky 🤩 ✅ Download PDB with SASA values in Re-Glyco Ensemble 🤩 Check it out!

Front page of Glycoshape website with the new background with floating SNFG symbols representing different monosaccharides. In the website the background is animated, so check it out at https://glycoshape.org

When you rebuild a glycosprotein with Re-Glyco Ensemble, now you can download the multiframe PDB with SASA values in the B-values column. The structure on the left shows in blue all the accessible surface and in light blue and red inaccessible residues due to the glycan presence. The buttons below are in cyan for regular multiframe PDB download (left) and download of all the file jobs (right) the middle gradient colored button allows users to download the PDB with SASA values

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Reposted by Ojas Singh

Elisa Fadda @elisafadda.bsky.social · 24/11/2025

Hello #glycotime! GlycoShape makes its debut on bsky today 🦋🎉 Follow us for news, updates and fun-facts (I take full responsibility for those, Ojas @ojas-singh.bsky.social 😆) below ⬇️

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Ben Schulz @benschulz.bsky.social · 09/09/2025

Super excited by our new #glycotime preprint! A long-term project from my group with awesome collaborator @elisafadda.bsky.social Regulation of N-glycosylation efficiency by eukaryotic oligosaccharyltransferase www.biorxiv.org/content/10.1... thread below 👇

media.tenor.com

a cartoon drawing of a pitcher and cup of sugar on a table

ALT: a cartoon drawing of a pitcher and cup of sugar on a table

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Elisa Fadda @elisafadda.bsky.social · 22/06/2025

When glycan recognition is linked to immune response, you need fine tuning! 😎 Here ⬇️ we show how human Siglecs act as molecular precision tools, recognising the glycan and also the biological environment (or context) these glycans are found in. A 1/5 #glycotime🧵 ⬇️ doi.org/10.1101/2025...

Schematic representation of the 14 human siglecs, 4 evolutionarily conserved on the left, with low sequence similarity, and 10 on the right sharing a higher sequence similarity to CD33. Siglec-6 is highlighted in yellow as it is the focus of this work. This is Figure 1 in the paper

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Reposted by Ojas Singh

Glyco@Alps @glyco-alps.bsky.social · 12/03/2025

Registration to our "Structural Glycoscience" Summer School is open !! Come to Grenoble for #glycotime lectures, practicals, visit to @esrf.fr @cermav.bsky.social and IBS. Information and registration at glycoalps.univ-grenoble-alpes.fr/news/summer-...

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Elisa Fadda @elisafadda.bsky.social · 13/12/2024

Glycoshape is 1 year old! 🎂🎁 🎉 Last year today we launched glycoshape.org after extensive consultation with a team of friends and colleagues. As head chef, it is my pleasure and duty to give a few thanks before the toast🥂 1/3

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Elisa Fadda @elisafadda.bsky.social · 11/12/2024

Christmas arrived early for me🎄🎁 just got a hard copy of the Nature Methods Nov 2024 issue with our GlycoShape article in it ❤️❤️ it smells sooo nice!!! 🤩🤣 doi.org/10.1038/s415...

Cover of Nov 2024 issue of Nature Methods (not our cover) showing an image of a section of a mouse intestine mostly yellow and green and cyan at the top, black background

Figure 1 (left) and figure 2 of our article

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Elisa Fadda @elisafadda.bsky.social · 13/11/2024

And the best poster award #SfG2024 goes to.....Ojas Singh @ojas-singh.bsky.social for his incredible work on GlycoShape!!!! 🎉🎊🎉🎊🎉🎊 Super congrats Ojas we are suuuper proud of you! #glycotime

Announcement of best posters awards at the SfG2024

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