Justin Westerfield
@justmwest.bsky.social
Postdoc in the Gunnar von Heijne lab @ Stockholm University. Studying membrane protein insertion and folding using biochemical and biophysical techniques 🧪
Progress report on my Relion bayesian polishing job on a local computer:
```
+ Performing loop over micrographs ...
166.67/166.67 hrs .....................~~(,_,">
+ Combining frames for micrographs ...
4.05/122.07 hrs .~~(,_,">
```
I think it's going well.
#CryoEM
```
+ Performing loop over micrographs ...
166.67/166.67 hrs .....................~~(,_,">
+ Combining frames for micrographs ...
4.05/122.07 hrs .~~(,_,">
```
I think it's going well.
#CryoEM
September 8, 2025 at 11:13 AM
Progress report on my Relion bayesian polishing job on a local computer:
```
+ Performing loop over micrographs ...
166.67/166.67 hrs .....................~~(,_,">
+ Combining frames for micrographs ...
4.05/122.07 hrs .~~(,_,">
```
I think it's going well.
#CryoEM
```
+ Performing loop over micrographs ...
166.67/166.67 hrs .....................~~(,_,">
+ Combining frames for micrographs ...
4.05/122.07 hrs .~~(,_,">
```
I think it's going well.
#CryoEM
Zotero finally has an Android app 🙌
August 9, 2025 at 7:09 AM
Zotero finally has an Android app 🙌
SULF's Doctoral Candidate Assocation warns internationals against starting a PhD Sweden and it seems like most of the complaint is with Migrationsverket, the Swedish Migration Agency. The negative effects of these excessive wait times are starting to pile up.
universitetslararen.se/2025/05/08/i...
universitetslararen.se/2025/05/08/i...
International PhD students advise against doctoral studies in Sweden - Universitetsläraren
Sweden is no longer an attractive country for international early-career researchers, says the SULF Doctoral Candidate Association in a new report.
universitetslararen.se
May 12, 2025 at 12:42 PM
SULF's Doctoral Candidate Assocation warns internationals against starting a PhD Sweden and it seems like most of the complaint is with Migrationsverket, the Swedish Migration Agency. The negative effects of these excessive wait times are starting to pile up.
universitetslararen.se/2025/05/08/i...
universitetslararen.se/2025/05/08/i...
May 12, 2025 at 12:32 PM
The program is out for the 2025 Membrane Protein Folding GRS! Applications are open until the end of May. Join us this June in Castelldefels, Spain!
🧪🧬🥼🔬
www.grc.org/membrane-pro...
🧪🧬🥼🔬
www.grc.org/membrane-pro...
2025 Membrane Protein Folding (GRS) Seminar GRC
The 2025 Gordon Research Seminar on Membrane Protein Folding (GRS) will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.
www.grc.org
April 30, 2025 at 2:05 PM
The program is out for the 2025 Membrane Protein Folding GRS! Applications are open until the end of May. Join us this June in Castelldefels, Spain!
🧪🧬🥼🔬
www.grc.org/membrane-pro...
🧪🧬🥼🔬
www.grc.org/membrane-pro...
Reposted by Justin Westerfield
Calling all membrane/membrane protein folks! Join us this summer in Barcelona for the Membrane Protein Folding Gordon Conference and Seminar. GRS chaired by @justmwest.bsky.social and myself! We are soliticiting abstracts from trainees for talks! Deadline - April 6.
www.grc.org/membrane-pro...
www.grc.org/membrane-pro...
2025 Membrane Protein Folding (GRS) Seminar GRC
The 2025 Gordon Research Seminar on Membrane Protein Folding (GRS) will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.
www.grc.org
March 26, 2025 at 3:01 PM
Calling all membrane/membrane protein folks! Join us this summer in Barcelona for the Membrane Protein Folding Gordon Conference and Seminar. GRS chaired by @justmwest.bsky.social and myself! We are soliticiting abstracts from trainees for talks! Deadline - April 6.
www.grc.org/membrane-pro...
www.grc.org/membrane-pro...
Proteins preferentially insert into membranes that have a similar hydrophobic thickness to the protein, even without cells or chaperones! Implies sufficiency of physical properties of membranes and proteins for proper sorting to organelles.
Cool paper! 🧪
doi.org/10.1038/s414...
Cool paper! 🧪
doi.org/10.1038/s414...
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes - Nature Communications
The organization of membrane proteins is critical to cellular function. Here the authors explore how computational protein design, MD simulation, and cell-free systems can be combined to elucidate how...
doi.org
January 31, 2025 at 8:14 AM
Proteins preferentially insert into membranes that have a similar hydrophobic thickness to the protein, even without cells or chaperones! Implies sufficiency of physical properties of membranes and proteins for proper sorting to organelles.
Cool paper! 🧪
doi.org/10.1038/s414...
Cool paper! 🧪
doi.org/10.1038/s414...
Very nice work outlining a new method to determine dimerization energies of TMDs in unbiased MD simulations 🧪
Check out our new paper!
Protein assembly in membranes is crucial yet elusive. Why steer when you can just observe? We introduce a bias-free simulation method that captures the full picture of transmembrane dimerization—free energies, mechanisms, and rates!
pubs.acs.org/doi/10.1021/...
Protein assembly in membranes is crucial yet elusive. Why steer when you can just observe? We introduce a bias-free simulation method that captures the full picture of transmembrane dimerization—free energies, mechanisms, and rates!
pubs.acs.org/doi/10.1021/...
Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simula...
pubs.acs.org
January 24, 2025 at 10:01 PM
Very nice work outlining a new method to determine dimerization energies of TMDs in unbiased MD simulations 🧪
My colleague and I are co-chairing the GRS on Membrane Protein Folding this Summer near Barcelona, Spain ⛱️
If you are a grad student or postdoc and work on membrane protein folding, apply!
www.grc.org/membrane-pro...
If you are a grad student or postdoc and work on membrane protein folding, apply!
www.grc.org/membrane-pro...
2025 Membrane Protein Folding (GRS) Seminar GRC
The 2025 Gordon Research Seminar on Membrane Protein Folding (GRS) will be held in Castelldefels, Barcelona Spain. Apply today to reserve your spot.
www.grc.org
January 24, 2025 at 6:50 PM
My colleague and I are co-chairing the GRS on Membrane Protein Folding this Summer near Barcelona, Spain ⛱️
If you are a grad student or postdoc and work on membrane protein folding, apply!
www.grc.org/membrane-pro...
If you are a grad student or postdoc and work on membrane protein folding, apply!
www.grc.org/membrane-pro...
I like my lab coats to feel like I'm wearing an armored vehicle but also a snuggie
January 23, 2025 at 2:21 PM
I like my lab coats to feel like I'm wearing an armored vehicle but also a snuggie
Just learned that one of the most productive scientists I know uses a cardboard box as a reference manager.
I'll be over here existentially questioning the value of my neatly curated zotero library.
I'll be over here existentially questioning the value of my neatly curated zotero library.
January 22, 2025 at 6:21 AM
Just learned that one of the most productive scientists I know uses a cardboard box as a reference manager.
I'll be over here existentially questioning the value of my neatly curated zotero library.
I'll be over here existentially questioning the value of my neatly curated zotero library.
chaotic neutral
January 15, 2025 at 1:59 PM
chaotic neutral
Beautiful night in Stockholm 🌃
November 13, 2024 at 9:35 PM
Beautiful night in Stockholm 🌃
If anyone knows of starter packs for biochemistry / biophysics, I would love to check them out!
November 10, 2024 at 11:20 AM
If anyone knows of starter packs for biochemistry / biophysics, I would love to check them out!
Goodreads has a popular list of books everyone should read. It's 33k books. Reading a book a day, this would take 90 years. Goodreads, this is not a serious list.
November 8, 2024 at 9:23 PM
Goodreads has a popular list of books everyone should read. It's 33k books. Reading a book a day, this would take 90 years. Goodreads, this is not a serious list.
Anyone familiar with BioPython? When I read a file with SeqIO, I see strange behavior.
If I assign a SeqRecord object to a variable, it is only iterable once. In the code below, the output is nothing, but if I switch the print statement to the first loop it prints fine.
What am I missing?
If I assign a SeqRecord object to a variable, it is only iterable once. In the code below, the output is nothing, but if I switch the print statement to the first loop it prints fine.
What am I missing?
July 26, 2024 at 1:38 PM
Anyone familiar with BioPython? When I read a file with SeqIO, I see strange behavior.
If I assign a SeqRecord object to a variable, it is only iterable once. In the code below, the output is nothing, but if I switch the print statement to the first loop it prints fine.
What am I missing?
If I assign a SeqRecord object to a variable, it is only iterable once. In the code below, the output is nothing, but if I switch the print statement to the first loop it prints fine.
What am I missing?
Something tells me they did not, in fact, read my preprint.
July 25, 2024 at 9:09 AM
Something tells me they did not, in fact, read my preprint.
Has anyone figured out how to name the individual chains for a job in the #Alphafold3 server? The output of a job with mutliple chains just has them labeled as A, B, C, etc.
June 2, 2024 at 4:03 PM
Has anyone figured out how to name the individual chains for a job in the #Alphafold3 server? The output of a job with mutliple chains just has them labeled as A, B, C, etc.