Negative stain: Wow, this protein is great! It's like shooting fish in a barrel

Cryo: Where did all the fish go? I swear I stocked all 6 barrels, 6 different ways, and then did that twice just to be sure. Not a single fish! I even used 3 different types of barrel

#structbio #cryoEM #gradschool #2lit2quit #virus

The best days #inthelab are when things don't work as expected and the result is even more interesting. I do not have time for this right now, but things are about to get real. #structbio
Side projects become main projects are the best

Hey, Structural Bio and Crystallography folks! Sign up for our FREE virtual user meeting for the #Hauptman-Woodward HTX Center!
Great talks! Lots of info! Open to everyone! March 31, bring your virtual structure-determining self and network with others in the structural biology community

#crystallography #structuralbiology #NationalHighThroughputCrystallizationCenter #structbio #proteinscience

Hey, Structural Bio and Crystallography folks! Sign up for our FREE virtual user meeting for the #Hauptman-Woodward HTX Center!
Great talks! Lots of info! Open to everyone! March 31, bring your virtual structure-determining self and network with others in the structural biology community

#crystallography #structuralbiology #NationalHighThroughputCrystallizationCenter #structbio #proteinscience

hmmmm, the "exlusome"

#structbio #molecularcell #Science

From: @bioRxiv_cellbiol
https://botsin.space/@bioRxiv_cellbiol/109956833473897972

Coming protein #macromolecular #crystallography #workshop in #Dubrovnik Coast (Croatia) April 16 to 21, 2023. https://htcc5.org/ 🇭🇷
Still participants slots available => do not hesitate to apply !
https://htcc5.org/2022/06/experimental-advances-in-macromolecular-crystallography/
#structbio #ccp4 #StrucuralBiology

New package! MRCFile.jl is a #JuliaLang parser for the MRC file format commonly used to store data like that produced by electron microscopy. #StructBio https://github.com/sethaxen/MRCFile.jl

I wrote this package for a project during my PhD and just now got around to registering it. I don't work with MRC files anymore, so if you do and are interested in co-maintaining, let me know!

“Beating the Best: Improving on AlphaFold2 at Protein Structure Prediction”

You can make AlphaFold2 better by jointly using it with RosettaFold. I am skeptical #StructBio #CASP

https://arxiv.org/abs/2301.07568

Inhouse #structbio #xray #diffraction this afternoon. Three projects.
1) Hmm, those "spots" are very smeary, as before
2) A couple of interesting, but probably protein, spots from @xtaldave 's small crystals, so off to #DLS_MX #synchrotron they go.
3) Ohhh, better than 1.9 Å, so lets collect a quick dataset before sending off to #synchrotron.

#elonmusk may be a duchecanoe but #tesla does make some good batteries.

Unexpected power outage (no inclement weather) today, but the #structbio server stayed live!

#homelab

#elonmusk may be a duchecanoe but #tesla does make some good batteries.

Unexpected power outage (no inclement weather) today, but the #structbio server stayed live!

#homelab

“Syntaxin 1 Ser14 phosphorylation is required for nonvesicular dopamine release”

MD simulations suggest the dopamine transporter can become a pore (?!) #MD #StructBio

https://www.science.org/doi/10.1126/sciadv.add8417

"Cyclic di-AMP traps proton-coupled K+ transporters of the KUP 1 family in an inward-occluded conformation"

Another structure of the #LeuT-fold potassium #transporter KimA shows how it is inhibited by cyclic di-AMP binding. #StructBio #CryoEM

https://www.biorxiv.org/content/10.1101/2023.01.09.523207v1

I have migrated my #Mastodon account to the new #structbio server:

https://struct.bio/@rdrighetto

Thanks @cryo2go for setting up the old and new servers and for the help with migration!

(also, testing cross-posting)

Is there anything like The Preprint Club in the #StructBio world? My impression is that these folks host a journal club, with one presenter in charge, and their discussion is summarized in writing and disseminated to the authors as a quasi-peer review document. However they only focus on #immunology papers; closest thing in my mind would be Biophysics Colab but I'm not sure if there is a discussion there.

https://www.preprintclub.com/

#preprint #openaccess

A quick look at the relentless pile of e-mails from during the end of year break.

You might think that the user, who was told that the function they wished to use in the crystal imaging software was broken, wouldn't try to use it on Boxing Day and then again on the New Year's BH but actually wait until being told it was fixed.

Problem is down to synchronisation issues migrating to new storage hardware so is unlikely to magically get better.

#Users #Christmas #IT #Structbio

“Structural titration reveals Ca2+-dependent conformational landscape of the IP3 receptor”

Awesome paper I’ll need to reread when I’m back at my desk. Global analysis of #cryoEM ensembles across many different conditions. Can someone from the #StructBio world tell me if these percentages are high-confidence enough to use to calculate Kd values? No error bars shown here.

https://www.biorxiv.org/content/10.1101/2022.12.29.522241v1

7/
Cyrus also recently co-founded the OpenFold consortium for biological AI with Prescient/Genentech, Arzeda, Outpace and help from AWS, to help provide fully open sourced platform models in molecular modeling (openfold.io).

#drugdiscovery #ai #proteinai #proteindesign #structbio

Learn more here:
Cyrusbio.com

... and other techniques. My main drive is to push #cryoET in tissues to enable #structbio in #devbio systems and get the throughput with modern #cryoFIB systems needed to do #visualproteomics. Also, from a “former lifetime” still very much into #MD #QMMM #proteindesign #CompChem

Redirecting my account from @qoto and joining @mstdn.science bc qoto cant cross post everywhere.
👋
#Biophysics #structbio #cryoEM #HIV #virology #academia #science