Yang Lee
@leetleyang.bsky.social
Lab boffin de l'ordinaire at Nxera Pharma erstwhile @mrclmb.bsky.social | Taking tips from tip boxes in the (only) correct order | #CryoEM #GPCR
Reposted by Yang Lee
Looking forward to the Grand Opening of the Northern Eye Imaging facility on 5th November at the Frederick Douglass Centre, Newcastle. Register now nusbf.ncl.ac.uk/ccpem-tfs-ne... for the latest #structuralbiology and #cryoem in the region, to see the new Tundra cryo-TEM and lots more!
October 21, 2025 at 11:25 AM
Looking forward to the Grand Opening of the Northern Eye Imaging facility on 5th November at the Frederick Douglass Centre, Newcastle. Register now nusbf.ncl.ac.uk/ccpem-tfs-ne... for the latest #structuralbiology and #cryoem in the region, to see the new Tundra cryo-TEM and lots more!
Reposted by Yang Lee
Rescaling FSC curves pubmed.ncbi.nlm.nih.gov/41059947/ #cryoem
October 10, 2025 at 1:15 AM
Rescaling FSC curves pubmed.ncbi.nlm.nih.gov/41059947/ #cryoem
Reposted by Yang Lee
Below (by @landerlab.bsky.social) is the 2nd #cryosparc recipe on @biorxivpreprint.bsky.social in a month. I remain worried about closed-source software affecting progress in #cryoEM. We should develop new algorithms instead!
#OpenSoftwareAcceleratesScience
www.biorxiv.org/content/10.1...
#OpenSoftwareAcceleratesScience
www.biorxiv.org/content/10.1...
www.biorxiv.org
October 5, 2025 at 8:20 AM
Below (by @landerlab.bsky.social) is the 2nd #cryosparc recipe on @biorxivpreprint.bsky.social in a month. I remain worried about closed-source software affecting progress in #cryoEM. We should develop new algorithms instead!
#OpenSoftwareAcceleratesScience
www.biorxiv.org/content/10.1...
#OpenSoftwareAcceleratesScience
www.biorxiv.org/content/10.1...
Reposted by Yang Lee
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 8:49 AM
Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching www.biorxiv.org/content/10.1101/2025.09.11.675606v1 #cryoem
Reposted by Yang Lee
Confidence-guided cryo-EM map optimisation with LocScale-2.0 www.biorxiv.org/content/10.1101/2025.09.11.674726v1 #cryoem
September 15, 2025 at 7:11 AM
Confidence-guided cryo-EM map optimisation with LocScale-2.0 www.biorxiv.org/content/10.1101/2025.09.11.674726v1 #cryoem
Reposted by Yang Lee
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
Reposted by Yang Lee
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!
Reposted by Yang Lee
Returned from a wonderful symposium in honour of the 50th anniversary of Richard Henderson's and Nigel Unwin's 1975 paper on the structure of bacteriorhodopsin - the paper that started the field of membrane protein structural biology.
Also fulfilled my dream of ringing the LMB seminar bell.
Also fulfilled my dream of ringing the LMB seminar bell.
July 12, 2025 at 12:10 PM
Returned from a wonderful symposium in honour of the 50th anniversary of Richard Henderson's and Nigel Unwin's 1975 paper on the structure of bacteriorhodopsin - the paper that started the field of membrane protein structural biology.
Also fulfilled my dream of ringing the LMB seminar bell.
Also fulfilled my dream of ringing the LMB seminar bell.
Reposted by Yang Lee
Ever wonder why SGD, which works so well for ab initio cryo-EM, never seems to get to high resolution on its own? Well, we have the answer: conditioning!
Work on SGD for high-resolution cryo-EM refinement from my previous postdoc finally published in @actacrystd.iucr.org
with Roy Lederman and @marcusabrubaker.bsky.social
📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...
with Roy Lederman and @marcusabrubaker.bsky.social
📜 Paper: journals.iucr.org/paper?S20597...
💻 Code: github.com/bogdantoader...
💾 Data: doi.org/10.5281/zeno...
June 24, 2025 at 9:31 PM
Ever wonder why SGD, which works so well for ab initio cryo-EM, never seems to get to high resolution on its own? Well, we have the answer: conditioning!
Reposted by Yang Lee
Standards for MicroED pubmed.ncbi.nlm.nih.gov/40539937/ #cryoem
June 21, 2025 at 6:41 PM
Standards for MicroED pubmed.ncbi.nlm.nih.gov/40539937/ #cryoem
Reposted by Yang Lee
Alves, Andrews, McBean, Wells, El-Gomati, Burkhalter, Schulze-Briese, Zambon, McMullan, Henderson, Russo, Jones: The Dublin Lens: A Cc=1.0 mm Objective Lens Intended for CryoEM at 100 keV https://arxiv.org/abs/2505.11458 https://arxiv.org/pdf/2505.11458 https://arxiv.org/html/2505.11458
May 19, 2025 at 6:14 AM
Alves, Andrews, McBean, Wells, El-Gomati, Burkhalter, Schulze-Briese, Zambon, McMullan, Henderson, Russo, Jones: The Dublin Lens: A Cc=1.0 mm Objective Lens Intended for CryoEM at 100 keV https://arxiv.org/abs/2505.11458 https://arxiv.org/pdf/2505.11458 https://arxiv.org/html/2505.11458
Reposted by Yang Lee
EtfD links beta oxidation to OxPhos in mycobacteria - recent work suggests that targeting EtfD could shorten #tubeculosis treatment.
But how does EtfD work? And how can you assay its activity?
In his final PhD manuscript @courbongautier.bsky.social provides answers!
www.biorxiv.org/content/10.1...
But how does EtfD work? And how can you assay its activity?
In his final PhD manuscript @courbongautier.bsky.social provides answers!
www.biorxiv.org/content/10.1...
May 16, 2025 at 2:30 PM
EtfD links beta oxidation to OxPhos in mycobacteria - recent work suggests that targeting EtfD could shorten #tubeculosis treatment.
But how does EtfD work? And how can you assay its activity?
In his final PhD manuscript @courbongautier.bsky.social provides answers!
www.biorxiv.org/content/10.1...
But how does EtfD work? And how can you assay its activity?
In his final PhD manuscript @courbongautier.bsky.social provides answers!
www.biorxiv.org/content/10.1...
Reposted by Yang Lee
1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.
April 27, 2025 at 8:49 PM
1/5: Over the last few months, I have been working on an update for the #FollowRelionGracefully dashboard, which offers improved real-time job previews for #cryoEM #Relion jobs.
Reposted by Yang Lee
Close to recreating it in ChimeraX:
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
April 16, 2025 at 6:31 AM
Close to recreating it in ChimeraX:
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
1. Install the python file: github.com/smsaladi/chi...
2. rainbow palette magma
3. col modify #1 blackness - 40
4. col modify #1 whiteness - 40
5. col modify #1 saturation - 50
6. col modify #1 lightness + 20
Room for improvement, needs more desaturation
Reposted by Yang Lee
Our paper is finally out: Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier | Science Advances www.science.org/doi/10.1126/...
#mitochondria #cryo-EM
#mitochondria #cryo-EM
Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier
The mitochondrial pyruvate carrier transport mechanism is ΔpH driven and is inhibited competitively by distinct compound classes.
www.science.org
April 18, 2025 at 6:16 PM
Our paper is finally out: Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier | Science Advances www.science.org/doi/10.1126/...
#mitochondria #cryo-EM
#mitochondria #cryo-EM
Reposted by Yang Lee
RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 11, 2025 at 7:54 PM
RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Yang Lee
Cool!
Molecular and functional profiling of Gαi as an intracellular pH sensor
www.nature.com/articles/s41...
Molecular and functional profiling of Gαi as an intracellular pH sensor
www.nature.com/articles/s41...
Molecular and functional profiling of Gαi as an intracellular pH sensor - Nature Communications
Here, the authors identify human Gαi protein as an intracellular pH sensor. The Gαi subunit undergoes a disorder to order transition as pH is increased over the intracellular pH range, which modulates...
www.nature.com
April 11, 2025 at 8:23 PM
Cool!
Molecular and functional profiling of Gαi as an intracellular pH sensor
www.nature.com/articles/s41...
Molecular and functional profiling of Gαi as an intracellular pH sensor
www.nature.com/articles/s41...
Reposted by Yang Lee
AlphaFold as a Prior: Experimental StructureDetermination Conditioned on a Pretrained Neural Network https://www.biorxiv.org/content/10.1101/2025.02.18.638828v1
February 22, 2025 at 2:49 AM
AlphaFold as a Prior: Experimental StructureDetermination Conditioned on a Pretrained Neural Network https://www.biorxiv.org/content/10.1101/2025.02.18.638828v1
Reposted by Yang Lee
We have an exciting opportunity for a new independent group leader with an interest in structural/molecular biology and machine learning to join our Division of Structural Studies at the @mrclmb.bsky.social! 🥳
Re-posts appreciated.
www.nature.com/naturecareer...
Re-posts appreciated.
www.nature.com/naturecareer...
Research Group Leader Tenure Track - Structural Studies - LMB 2549 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12835196
Research Group Leader Tenure Track Starting Salary £65,940 to £74,448 per annum MRC Laboratory of Molecular Biology, Cambridge, UK
www.nature.com
January 27, 2025 at 9:38 AM
We have an exciting opportunity for a new independent group leader with an interest in structural/molecular biology and machine learning to join our Division of Structural Studies at the @mrclmb.bsky.social! 🥳
Re-posts appreciated.
www.nature.com/naturecareer...
Re-posts appreciated.
www.nature.com/naturecareer...
Reposted by Yang Lee
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
January 19, 2025 at 4:40 PM
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
Reposted by Yang Lee
We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!
January 19, 2025 at 12:15 PM
We processed the results of the BindCraft user experience poll and we are quite happy with how it turned out. We had over 60 responses from many different users, turns about about a quarter are from industry and a quarter of users run it via Google Colab!
Reposted by Yang Lee
Off-axis electron holography of unstained bacteriophages: Toward electrostatic potential measurement of biological samples pubmed.ncbi.nlm.nih.gov/39818354/
January 18, 2025 at 2:59 AM
Off-axis electron holography of unstained bacteriophages: Toward electrostatic potential measurement of biological samples pubmed.ncbi.nlm.nih.gov/39818354/
Reposted by Yang Lee
Proud to share our work spear-headed by PhD student Tommy Sroka with major contributions by #xenopus expert Kerstin Feistel.
Our iAPEX #ProximityLabeling method for #MassSpec based subcellular #proteomics works by locally generating H2O2 using a D-amino acid oxidase that activates APEX2 in situ.
Our iAPEX #ProximityLabeling method for #MassSpec based subcellular #proteomics works by locally generating H2O2 using a D-amino acid oxidase that activates APEX2 in situ.
iAPEX: Improved APEX-based proximity labeling for subcellular proteomics using an enzymatic reaction cascade
Ascorbate peroxidase (APEX) is a versatile labeling enzyme used for live-cell proteomics at high spatial and temporal resolution. However, toxicity of its substrate hydrogen peroxide and background la...
www.biorxiv.org
January 11, 2025 at 7:51 PM
Proud to share our work spear-headed by PhD student Tommy Sroka with major contributions by #xenopus expert Kerstin Feistel.
Our iAPEX #ProximityLabeling method for #MassSpec based subcellular #proteomics works by locally generating H2O2 using a D-amino acid oxidase that activates APEX2 in situ.
Our iAPEX #ProximityLabeling method for #MassSpec based subcellular #proteomics works by locally generating H2O2 using a D-amino acid oxidase that activates APEX2 in situ.
Reposted by Yang Lee
In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:
January 17, 2025 at 6:43 PM
In a great collaboration with @hummerlab.bsky.social and the Kräusslich lab: HIV capsid doesn't break at the NPC; instead, it cracks open the NPC itself! Details in Cell: authors.elsevier.com/sd/article/S... @mpibp.bsky.social @uniheidelberg.bsky.social A thread below:
Reposted by Yang Lee
Gave our first state of the lab address this week. I broke down the cost of science, from people to stuff. Dove into spending compared to budgets. Spent time on grant submissions and manuscript/project expectations for the year.
I want to be as transparent as possible & this was a great start! 🧪🧠👩🔬
I want to be as transparent as possible & this was a great start! 🧪🧠👩🔬
January 18, 2025 at 4:12 PM
Gave our first state of the lab address this week. I broke down the cost of science, from people to stuff. Dove into spending compared to budgets. Spent time on grant submissions and manuscript/project expectations for the year.
I want to be as transparent as possible & this was a great start! 🧪🧠👩🔬
I want to be as transparent as possible & this was a great start! 🧪🧠👩🔬