GlycoShape
@glycoshape.org
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
This ⬇️ is screenshot of the Advanced Settings I used to produce the ensemble shown in the picture above,
January 3, 2026 at 7:59 PM
This ⬇️ is screenshot of the Advanced Settings I used to produce the ensemble shown in the picture above,
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,
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,
January 3, 2026 at 7:53 PM
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,
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,
GlycoShape couldn't have happened without all the hard work, super skillzzz and dedication of our team, current (below) and previous members! 🤩🤩 EF is not the only cat, you can scroll over the photos to discover all others 😍 And key funding from @researchireland.ie (former SFI) FFP🙏 ⬇️🧵
December 15, 2025 at 11:39 AM
GlycoShape couldn't have happened without all the hard work, super skillzzz and dedication of our team, current (below) and previous members! 🤩🤩 EF is not the only cat, you can scroll over the photos to discover all others 😍 And key funding from @researchireland.ie (former SFI) FFP🙏 ⬇️🧵
We have used this approach to rebuild hyperglycosylated human EPO (or NESP shown below in the gif) in seconds 🏎️💨 as part of MSci and postgraduate summer schools structure glycoengineering for biologics workshop ⬇️🧵
December 15, 2025 at 11:31 AM
We have used this approach to rebuild hyperglycosylated human EPO (or NESP shown below in the gif) in seconds 🏎️💨 as part of MSci and postgraduate summer schools structure glycoengineering for biologics workshop ⬇️🧵
We have also a new and improved Re-Glyco Ensemble, where you can see through a multiframe (50 to 500 frames from MD) glycan structure view, statistics and corresponding SASA analysis how the protein structure shifts the conformational equilibrium of the glycans ⬇️🧵
December 15, 2025 at 11:27 AM
We have also a new and improved Re-Glyco Ensemble, where you can see through a multiframe (50 to 500 frames from MD) glycan structure view, statistics and corresponding SASA analysis how the protein structure shifts the conformational equilibrium of the glycans ⬇️🧵
We are not only continuing to grow our library, but also continuously perfecting and expanding our tools. Re-Glyco is leading the way 🤩, with improved computational efficiency 🏎️💨 and informative queuing widget and calculation process log ⬇️🧵
December 15, 2025 at 11:06 AM
We are not only continuing to grow our library, but also continuously perfecting and expanding our tools. Re-Glyco is leading the way 🤩, with improved computational efficiency 🏎️💨 and informative queuing widget and calculation process log ⬇️🧵
To do that we built the largest OA 3D library of glycan structures worldwide 🤯, counting 882 unique glycans complemented by at least 3 conformers each to account for their dynamics, obtained from the analysis of multimicrosecond MD simulations doi.org/10.1038/s415... ⬇️🧵
December 15, 2025 at 10:55 AM
To do that we built the largest OA 3D library of glycan structures worldwide 🤯, counting 882 unique glycans complemented by at least 3 conformers each to account for their dynamics, obtained from the analysis of multimicrosecond MD simulations doi.org/10.1038/s415... ⬇️🧵
Since Dec 2023 Glycoshape has progressively built a community of glycoengineers that continues to grow. These scientists recognise that to understand glycoproteins structure and function we need to take into consideration the glycans they have, with their micro and macro heterogeneity 🧵⬇️
December 15, 2025 at 10:46 AM
Since Dec 2023 Glycoshape has progressively built a community of glycoengineers that continues to grow. These scientists recognise that to understand glycoproteins structure and function we need to take into consideration the glycans they have, with their micro and macro heterogeneity 🧵⬇️
Happy birthday to us! 🥂🎂🥳 We are only 2 yo, but so much #glycotime happened since Dec 2023! ⬇️🧵
We truly appreciate your support, you fabulous glycoengineers around the world and we have so many exciting new tools for you coming up in 2026 to make your 3D glycoforms even better and faster! 🤩
We truly appreciate your support, you fabulous glycoengineers around the world and we have so many exciting new tools for you coming up in 2026 to make your 3D glycoforms even better and faster! 🤩
December 15, 2025 at 10:37 AM
Happy birthday to us! 🥂🎂🥳 We are only 2 yo, but so much #glycotime happened since Dec 2023! ⬇️🧵
We truly appreciate your support, you fabulous glycoengineers around the world and we have so many exciting new tools for you coming up in 2026 to make your 3D glycoforms even better and faster! 🤩
We truly appreciate your support, you fabulous glycoengineers around the world and we have so many exciting new tools for you coming up in 2026 to make your 3D glycoforms even better and faster! 🤩
This insight does not substitute MD simulations at all, but can complement it for high throughput as it took us seconds to build the structures you see with Re-Glyco Ensemble, about 30 mins to investigate and run rotameric search, and a whole lot of time to play around with pretty pictures 🤓 ⬇️🧵
December 11, 2025 at 12:28 PM
This insight does not substitute MD simulations at all, but can complement it for high throughput as it took us seconds to build the structures you see with Re-Glyco Ensemble, about 30 mins to investigate and run rotameric search, and a whole lot of time to play around with pretty pictures 🤓 ⬇️🧵
Fucosylation does not change that, but it makes the fold less compact as it sits between the a6 arm and the core. The presence of fucose in this case allows the glycan to access all its preferred conformational degrees of freedom around the pocket indicated by a circle ⬇️🧵
December 11, 2025 at 12:18 PM
Fucosylation does not change that, but it makes the fold less compact as it sits between the a6 arm and the core. The presence of fucose in this case allows the glycan to access all its preferred conformational degrees of freedom around the pocket indicated by a circle ⬇️🧵
We see (with just 50 frames from multimicrosecond MD data available in the database) that the conformation of the non-fucosylated glycan (G44826KU) is restricted by the protein structure. Indeed, the a6 arm (esp with gal and sia) prefers to fold over the core ⬇️🧵 doi.org/10.1093/glyc...
December 11, 2025 at 12:10 PM
We see (with just 50 frames from multimicrosecond MD data available in the database) that the conformation of the non-fucosylated glycan (G44826KU) is restricted by the protein structure. Indeed, the a6 arm (esp with gal and sia) prefers to fold over the core ⬇️🧵 doi.org/10.1093/glyc...
Glycans structure and flexibility is an inherent property of their structure and branching. The conformational equilibrium is only shifted when the protein architecture requires a selection of conformers that complement it best. This appears to be one of those cases
December 11, 2025 at 11:59 AM
Glycans structure and flexibility is an inherent property of their structure and branching. The conformational equilibrium is only shifted when the protein architecture requires a selection of conformers that complement it best. This appears to be one of those cases
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!
✅ 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!
December 5, 2025 at 12:23 PM
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!
✅ 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!
This unique modification is introduced by the tryptophan C-mannosyltransferase (CMT). The beautiful structure of the C elegans CMT and the reaction are described in the brilliant work of Joël Bloch and coworkers[1].
December 4, 2025 at 7:10 PM
This unique modification is introduced by the tryptophan C-mannosyltransferase (CMT). The beautiful structure of the C elegans CMT and the reaction are described in the brilliant work of Joël Bloch and coworkers[1].
For some unique #glycotime: C-man is a rare (but evolutionarily very old[1]) post translational modification of proteins, where the C2 of Trp in W-x-x-W/C sequons are linked to a single man through a C-C bond 🤯 This and its position within the structure stabilises the (unusual for man) 1C4 chair[2]
December 4, 2025 at 6:52 PM
For some unique #glycotime: C-man is a rare (but evolutionarily very old[1]) post translational modification of proteins, where the C2 of Trp in W-x-x-W/C sequons are linked to a single man through a C-C bond 🤯 This and its position within the structure stabilises the (unusual for man) 1C4 chair[2]
3/3 GlycoShape is an open access library of glycan structures from MD simulations that gives users all the diff structures significantly occupied at equilibrium and tools to reconstruct the target glycoproteins with a single representative conformer (Re-Glyco) or multiple (Re-Glyco Ensemble)
December 2, 2025 at 6:28 PM
3/3 GlycoShape is an open access library of glycan structures from MD simulations that gives users all the diff structures significantly occupied at equilibrium and tools to reconstruct the target glycoproteins with a single representative conformer (Re-Glyco) or multiple (Re-Glyco Ensemble)
2/3 Glycans aren't genetically encoded (non-templated), so they can be quite heterogeneous.
This is a problem especially in cryo-EM studies of glycoproteins, where you can assign clearly the common denominator and most rigid part of the glycan, usually the bit linked to the aglycon
This is a problem especially in cryo-EM studies of glycoproteins, where you can assign clearly the common denominator and most rigid part of the glycan, usually the bit linked to the aglycon
December 2, 2025 at 5:50 PM
2/3 Glycans aren't genetically encoded (non-templated), so they can be quite heterogeneous.
This is a problem especially in cryo-EM studies of glycoproteins, where you can assign clearly the common denominator and most rigid part of the glycan, usually the bit linked to the aglycon
This is a problem especially in cryo-EM studies of glycoproteins, where you can assign clearly the common denominator and most rigid part of the glycan, usually the bit linked to the aglycon
Tuesday #glycotime 🥄🍬
Glycans are a 🔝 example of "disordered" molecules. Inherent flexibility prevents sugars from adopting fixed, unique 3D positions relative to the crystal lattice, so they often are invisible to X-ray diffraction, unless they are bound and thus restrained in place 1/3 🧵
Glycans are a 🔝 example of "disordered" molecules. Inherent flexibility prevents sugars from adopting fixed, unique 3D positions relative to the crystal lattice, so they often are invisible to X-ray diffraction, unless they are bound and thus restrained in place 1/3 🧵
December 2, 2025 at 5:36 PM
Tuesday #glycotime 🥄🍬
Glycans are a 🔝 example of "disordered" molecules. Inherent flexibility prevents sugars from adopting fixed, unique 3D positions relative to the crystal lattice, so they often are invisible to X-ray diffraction, unless they are bound and thus restrained in place 1/3 🧵
Glycans are a 🔝 example of "disordered" molecules. Inherent flexibility prevents sugars from adopting fixed, unique 3D positions relative to the crystal lattice, so they often are invisible to X-ray diffraction, unless they are bound and thus restrained in place 1/3 🧵
It's Fucose Friday 🔺, the best #glycotime of the week!
Fucose is commonly found as a glycan modification, but it can be linked directly to proteins as O-fucose 😎
Here ⬇️ O-fucosylation of TSR1 by POFUT2 in the ER stabilises the TSRs characteristic fold 🤩
pmc.ncbi.nlm.nih.gov/articles/PMC...
Fucose is commonly found as a glycan modification, but it can be linked directly to proteins as O-fucose 😎
Here ⬇️ O-fucosylation of TSR1 by POFUT2 in the ER stabilises the TSRs characteristic fold 🤩
pmc.ncbi.nlm.nih.gov/articles/PMC...
November 28, 2025 at 7:07 PM
It's Fucose Friday 🔺, the best #glycotime of the week!
Fucose is commonly found as a glycan modification, but it can be linked directly to proteins as O-fucose 😎
Here ⬇️ O-fucosylation of TSR1 by POFUT2 in the ER stabilises the TSRs characteristic fold 🤩
pmc.ncbi.nlm.nih.gov/articles/PMC...
Fucose is commonly found as a glycan modification, but it can be linked directly to proteins as O-fucose 😎
Here ⬇️ O-fucosylation of TSR1 by POFUT2 in the ER stabilises the TSRs characteristic fold 🤩
pmc.ncbi.nlm.nih.gov/articles/PMC...
To wish our friend and main O-glycan 3D structure contributor extraordinaire @silviadandrea.bsky.social all the best with the submission of her PhD thesis tomorrow, today's 🥄🍬 is dedicated to sialic acid 💜 with a mini 🧵 about all the wonderful functions Silvia worked on
November 27, 2025 at 6:14 PM
To wish our friend and main O-glycan 3D structure contributor extraordinaire @silviadandrea.bsky.social all the best with the submission of her PhD thesis tomorrow, today's 🥄🍬 is dedicated to sialic acid 💜 with a mini 🧵 about all the wonderful functions Silvia worked on
Today we used Re-Glyco to rebuild human EPO from AF-P01588 with glycosylation selected from Lippold et al [10.1021/acs.analchem.0c01794] From the 3D structure we identified ideal locations for extra N-glycans, some of which are actually in NESP [10.1054/bjoc.2001.1746]
Super fun 3D edu #glycotime!
Super fun 3D edu #glycotime!
![title slide of the workshop held today for the Advance Pharmacology module at the University of Southampton (E. Fadda lecturer and coordinator) right-hand side in the bubble, human EPO (grey) with glycosylation reconstructed according to [10.1021/acs.analchem.0c01794] bound to the EPO receptor (cyan) in PDB 1CN4. Slide background is blue](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:xorrvcukxonsyeoudfzmnmhz/bafkreiactex7lfbmup6a3e7ezk4rao6zq4zvnbpprgkvuk4buvghhbqy6a@jpeg)
November 26, 2025 at 3:28 PM
Today we used Re-Glyco to rebuild human EPO from AF-P01588 with glycosylation selected from Lippold et al [10.1021/acs.analchem.0c01794] From the 3D structure we identified ideal locations for extra N-glycans, some of which are actually in NESP [10.1054/bjoc.2001.1746]
Super fun 3D edu #glycotime!
Super fun 3D edu #glycotime!
1/2 Check out the page of your fav glycan in @glycosmos.bsky.social which also has all the 3D info our database[2] and a direct link to its page in GlycoShape. Makes it very easy to see how many 3D structures correspond to a single 2D structure! 😉
November 25, 2025 at 9:10 AM
1/2 Check out the page of your fav glycan in @glycosmos.bsky.social which also has all the 3D info our database[2] and a direct link to its page in GlycoShape. Makes it very easy to see how many 3D structures correspond to a single 2D structure! 😉
To welcome our new friends, first spoonful of sugar 🥄🍬
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
November 25, 2025 at 9:02 AM
To welcome our new friends, first spoonful of sugar 🥄🍬
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵
Glycan structures can be very complex and deceivingly similar, yet they have unique GlyTouCan IDs[1] that you can find by drawing the glycan you need in gb.glytoucan.org or in the glycoshape.org sugar drawer 1/3 🧵