Jan-Hannes Schaefer
@jhschaef.bsky.social
Structural Biology to the rescue. Postdoc at Scripps Research. ❄️🔬 🎹⛳
In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...
December 17, 2025 at 4:00 PM
In our new preprint, we show how fibril-dynamics of signaling component TIRAP supports sensitive & fast sensing of endotoxin LPS. Congrats to co-lead @arthurfelker.bsky.social. @piehlerlab.bsky.social @arnemoeller.bsky.social #TLR #cryoEM #blender doi.org/10.64898/202...
Thanks to @actacrystf.iucr.org for highlighting our smart 2D selection tool CryoSift. You can test it yourself here cryosift.org
December 11, 2025 at 4:48 PM
Thanks to @actacrystf.iucr.org for highlighting our smart 2D selection tool CryoSift. You can test it yourself here cryosift.org
Reposted by Jan-Hannes Schaefer
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Jan-Hannes Schaefer
Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier!
I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
November 25, 2025 at 6:26 PM
Just installed Doppio on our Linux machine. This is awesome work making relion more accessible and easy to run. I haven't tried submitting jobs yet but it is already making our live easier!
I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
I met Matt Iadanza at the CZI but I guess he doesn't have bluesky to tag!
CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!
November 7, 2025 at 4:58 PM
CryoSift is now out @actacrystf.iucr.org doi.org/10.1107/S205... Thanks to all involved. Happy processing!
Reposted by Jan-Hannes Schaefer
Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale ##ElectronMicroscopy##CryoEM##TimeResolvedStudies... ##IUCrhttps://journals.iucr.org/paper?S2052252525008838
`Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale
The development of methods for low-cost time-resolved cryo-EM using an on-grid mixing strategy is described.
journals.iucr.org
October 28, 2025 at 1:00 AM
Lauren Alexandrescu et al.: `Mix-it-up': accessible time-resolved cryo-EM on the millisecond timescale ##ElectronMicroscopy##CryoEM##TimeResolvedStudies... ##IUCrhttps://journals.iucr.org/paper?S2052252525008838
Reposted by Jan-Hannes Schaefer
Excited to share a new chapter of my scientific journey in Chris Russo's group — developing a way to freeze proteins faster than they diffuse, paving the way for cryo-EM without air–water interface damage.
Chris Russo and Anastasiia Gusach have developed a new method to prepare #cryoEM samples that avoids protein damage during freezing
Read more: www2.mrc-lmb.cam.ac.uk/a-new-method...
#LMBResearch
Read more: www2.mrc-lmb.cam.ac.uk/a-new-method...
#LMBResearch
October 22, 2025 at 9:33 PM
Excited to share a new chapter of my scientific journey in Chris Russo's group — developing a way to freeze proteins faster than they diffuse, paving the way for cryo-EM without air–water interface damage.
Reposted by Jan-Hannes Schaefer
🚀 Introducing fully automated data processing for repeat-target #cryoEM.
Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention.
Preprint: www.biorxiv.org/content/10.1...
Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention.
Preprint: www.biorxiv.org/content/10.1...
October 20, 2025 at 2:32 PM
🚀 Introducing fully automated data processing for repeat-target #cryoEM.
Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention.
Preprint: www.biorxiv.org/content/10.1...
Using new tools in #CryoSPARC, it is now possible to obtain resolutions & map quality equal to or better than manual processing, with zero user intervention.
Preprint: www.biorxiv.org/content/10.1...
Thanks @odedrechavi.bsky.social. Even without explicit coverage of structural biology, it did a great job as Reviewer #0 on my latest preprint. Highly recommend www.qedscience.com
October 17, 2025 at 3:43 PM
Thanks @odedrechavi.bsky.social. Even without explicit coverage of structural biology, it did a great job as Reviewer #0 on my latest preprint. Highly recommend www.qedscience.com
I'll try and keep you updated. The story continues.
October 5, 2025 at 6:17 PM
I'll try and keep you updated. The story continues.
@maxewilkinson.bsky.social fun little cryo-EM puzzle. I am still pushing the resolution to let ModelAngelo do its magic. My guess was either a common amyloid binder like SAP or an intermediate of Lysozyme-amyloids...
October 5, 2025 at 5:27 PM
@maxewilkinson.bsky.social fun little cryo-EM puzzle. I am still pushing the resolution to let ModelAngelo do its magic. My guess was either a common amyloid binder like SAP or an intermediate of Lysozyme-amyloids...
Thanks @olibclarke.bsky.social I must have overlooked that one and should give it a go.
October 5, 2025 at 1:58 PM
Thanks @olibclarke.bsky.social I must have overlooked that one and should give it a go.
Reprocessed ALys Amyloids from EMPIAR-11785 Fändrich Lab
October 5, 2025 at 4:24 AM
Reprocessed ALys Amyloids from EMPIAR-11785 Fändrich Lab
CS workflow for easy testing: github.com/schaefer-jh/...
GitHub - schaefer-jh/CS-amyloids: Amyloid-processing with cryo-SPARC
Amyloid-processing with cryo-SPARC. Contribute to schaefer-jh/CS-amyloids development by creating an account on GitHub.
github.com
October 5, 2025 at 4:19 AM
CS workflow for easy testing: github.com/schaefer-jh/...
Helical Reconstruction of Amyloids in cryoSPARC?
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
October 5, 2025 at 4:16 AM
Helical Reconstruction of Amyloids in cryoSPARC?
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
We present guidelines, limitations & future perspectives for processing amyloids in cryoSPARC @structurabio.bsky.social.
Great collaboration of the Kelly Lab and @landerlab.bsky.social #cryoEM #amyloid www.biorxiv.org/content/10.1...
Reposted by Jan-Hannes Schaefer
We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends
landaulabcssb.bsky.social
landaulabcssb.bsky.social
September 26, 2025 at 3:18 PM
We had a fantastic time hosting the first Functional Amyloid Meeting @ DESY! #FFFatDESY2025 #FunctionalFibrilFriends
landaulabcssb.bsky.social
landaulabcssb.bsky.social
Reposted by Jan-Hannes Schaefer
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
September 26, 2025 at 2:28 AM
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
Reposted by Jan-Hannes Schaefer
❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology
Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification https://www.biorxiv.org/content/10.1101/2025.09.14.676144v1
September 18, 2025 at 8:04 AM
❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology
Reposted by Jan-Hannes Schaefer
Another successful approach to the same problem as HR-HAIR! 🤩 I wonder if a combo might be worth a try - use one frequency band to get perfectly centered particles using 2DTM, then re-estimate orientations using HR-HAIR with a non-overlapping frequency band?
Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoem
September 17, 2025 at 10:57 AM
Another successful approach to the same problem as HR-HAIR! 🤩 I wonder if a combo might be worth a try - use one frequency band to get perfectly centered particles using 2DTM, then re-estimate orientations using HR-HAIR with a non-overlapping frequency band?
A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
10 Rules for a Structural Bioinformatic Analysis
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...
chemrxiv.org
September 13, 2025 at 3:35 PM
A great resource. One highlight for me is: "One of the best things about structural biology is visualizing what you are discovering."
Reposted by Jan-Hannes Schaefer
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
September 13, 2025 at 12:05 AM
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
Congrats @olibclarke.bsky.social, great work. I've tried PKA and failed. SPA processing is still an art and lesson in persistence.
September 13, 2025 at 5:53 AM
Congrats @olibclarke.bsky.social, great work. I've tried PKA and failed. SPA processing is still an art and lesson in persistence.
Magellon has taken off to explore your cryo-EM data! Now out in @iucrj.iucr.org doi.org/10.1107/S205... Congrats to all involved!
September 5, 2025 at 2:48 PM
Magellon has taken off to explore your cryo-EM data! Now out in @iucrj.iucr.org doi.org/10.1107/S205... Congrats to all involved!
I often go back to this striking study: doi.org/10.1126/scie...
September 4, 2025 at 1:18 AM
I often go back to this striking study: doi.org/10.1126/scie...
Been thinking about creating a collection of good protein structure figures, as inspiration for my own work.
#1 www.nature.com/articles/s41...
#1 www.nature.com/articles/s41...
September 4, 2025 at 1:09 AM