osvalb.bsky.social
Osvaldo Burastero
@osvalb.bsky.social
850 followers 940 following 25 posts
Biophysics enthusiast. Currently focused on data analysis: https://spc.embl-hamburg.de
spc.embl-hamburg.de
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spcembl.bsky.social
SPC Facility & Garcia-Alai Lab @spcembl.bsky.social · 22d
@mpimarinemicrobio.bsky.social @cssbhamburg.bsky.social
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Reposted by Osvaldo Burastero
spcembl.bsky.social
SPC Facility & Garcia-Alai Lab @spcembl.bsky.social · 24d
We’re looking for a GL!

Join us at EMBL Hamburg! 🧫🦠🧬

The position will be based at CSSB @cssbhamburg.bsky.social , an interdisciplinary research centre focused on infection biology, and will be integrated into EMBL's research programme. @embl.org

Find out more and apply here: lnkd.in/dJU9pee7
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Reposted by Osvaldo Burastero
embl.org
EMBL @embl.org · Aug 14
EMBL-EBI ARISE fellow @melanieschneider.bsky.social & EMBL Grenoble’s Marquez team developed EnsembleFlex 🖥️! It can analyse flexibility, identify protein states, and show drug binding, providing new insights into protein dynamics!
doi.org/10.1016/j.st...
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Aug 13
Do you want to analyze mass photometry (MP) count data with Python scripts? Try pyPhotoMol, a package to process, fit, and visualize the MP data 👨‍💻

github.com/osvalB/pypho...

pyPhotoMol is derived from PhotoMol, our web tool for MP:

spc.embl-hamburg.de/app/photoMol

#massphotometry #Python #code
Simulated mass photometry results showing count distributions at a constant concentration of A (150 kDa) and seven different concentrations of B (30 kDa). B free is under the limit of detection (40 kDa). A and B interact with an equilibrium dissociation constant (Kd) of 1 nM. Screenshot of the pyPhotoMol package repository (https://github.com/osvalB/pyphotomol)
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Osvaldo Burastero @osvalb.bsky.social · Jun 12
Happy to present the next tool under development. KinGenie, for binding kinetics. It already supports biolayer interferometry input files. Try it here: spc.embl-hamburg.de
🎉🎉🧪🧪
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Apr 28
ChiraKit, our tool for circular dichroism, has been published in NAR 🎉🎉👨‍🔬👨‍🔬. @narjournal.bsky.social
spcembl.bsky.social
SPC Facility & Garcia-Alai Lab @spcembl.bsky.social · Apr 28
🔊 Thrilled to share our latest work, just published in NAR! 📃

We present ChiraKit, open-source tool to process raw CD data and perform advanced analysis!

Access via our eSPC web-server!

➡️ spc.embl-hamburg.de
@osvalb.bsky.social @lucasdefelipe.bsky.social @embl.org @cssbhamburg.bsky.social
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Reposted by Osvaldo Burastero
cczekster.bsky.social
Clarissa Czekster @cczekster.bsky.social · Apr 24
Just want to say thanks to @spcembl.bsky.social for developing ChiraKit and allowing quick and informative analysis of CD data - more here www.biorxiv.org/content/10.1...
best news of the day today as we were stuck with beautiful but hard to analyze data 🙂 #scienceisawesome
ChiraKit, an online tool for the analysis of circular dichroism spectroscopy data
Circular dichroism (CD) spectroscopy is an established biophysical technique to study chiral molecules. CD allows investigating conformational changes under varying experimental conditions and has bee...
www.biorxiv.org
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Feb 14
Interested in antimicrobial resistance and drug discovery? Attend the talk of my colleague and partner Tania Szal 😊
Monday 17th at 8:30. Platform: protein-small molecule interactions I
#BPS2025
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Feb 14
Looking forward to making new connections at #BPS2025👨 Meet me at poster B38 on Tuesday 18 Feb 13:45. Session "protein stability folding and chaperones"
espc poster details BPS conference banner
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Feb 11
Just finished a science poster (in Figma) and wanted to share the template I used! 🎨 Hope it's useful: github.com/osvalB/figma...
Poster template done in Figma
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Reposted by Osvaldo Burastero
embl.org
EMBL @embl.org · Feb 3
Scientists at University of Buenos Aires, EMBL Hamburg, and others mapped yerba mate’s genome, providing surprising facts about its biochemistry and evolution of caffeine biosynthesis. 🧉🧬🧪

Find out more: www.embl.org/news/science...

@spcembl.bsky.social
A cup of yerba mate on a wooden surface and some dried yerba mate next to it.
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
Curious fact: many researchers normalise the CD signal using the number of residues. Others, use the number of peptide bonds. Still, everyone calls it 'mean residue molar ellipticity/extinction'. The cromophore unit is the peptide bond, so use that. For short peptides, it matters. 👍
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
After many months of gathering user feedback and improving our software, we think it's time to share it with the community. Enjoy our latest tool 🥳 , and stay tuned for the next one 😉
spcembl.bsky.social
SPC Facility & Garcia-Alai Lab @spcembl.bsky.social · Jan 31
🔊 Our latest biophysical tool for circular dichroism analysis, ChiraKit, is out 🔍

To read more about it, visit www.biorxiv.org/content/10.1...

ChiraKit can be accessed at spc.embl-hamburg.de

@osvalb.bsky.social @lucasdefelipe.bsky.social @embl.org @cssbhamburg.bsky.social
@mosbri.bsky.social
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
The estimated Kd (micromolar) is 1.3, and we also provide the asymmetric confidence interval: [0.5 - 3.1] (link.springer.com/article/10.1...)

The reported Kd by the authors was 1.2.

6. Extra: I scaled the plot to start around 0.
Points: measured MST signal. Line: Fitted curved based on the estimated Kd of 1.3 micromolar.
osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
4. Go to the '2. Fitting' section. Inside the 'Advanced settings', set the Kd max value to 5 micromolar (to help the fitting algorithm 😄😬 ).

5. Press on 'Run fitting' and voila!
Screenshot of ThermoAffinity showing that the Kd upper bound (for the fitting) is 5 micromolar.
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
ThermoAffinity - Default
spc.embl-hamburg.de
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
2. Import the file into our tool ThermoAffinity (spc.embl-hamburg.de/app/thermoAf...)

3. Set the units to 'Nanomolar' and the hot region between 14 - 20 seconds (based on what the authors reported)
Screenshot of ThermoAffinity showing that the selected units are 'Nanomolar', and that the hot region interval goes from 14 to 20 seconds. Microscale thermophoresis traces of the entry https://mbdb-data.org/mst/5s81t-w6s49
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
Hope this makes it easier to reproduce published analyses. A short example (circa 10 minutes):

1. Downloaded the microscale thermophoresis raw data Lys VHH B09 25 nM Lys100uM max_MSTTraceRawData.xlsx, available at
mbdb-data.org/mst/5s81t-w6...
Molecular Biophysics Database
mbdb-data.org
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 31
Our colleagues in Prague have released a database for molecular biophysics data - mbdb-data.org! 🌍📊 A great step forwards FAIR data in biophysics. 🙌✨ @mosbri.bsky.social
Molecular Biophysics Database
mbdb-data.org
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instruct-eric.bsky.social
Instruct-ERIC @instruct-eric.bsky.social · Jan 30
Instruct now has two R&D calls open - aimed at growing and advancing the global structural biology toolkit!

- The pilot award is open to Early Career Researchers, with up to €15,000 available for any topic
- The TechDev call in AI research awards up to €30,000

instruct-eric.org/rd-project-a...
R&D project awards - Instruct-ERIC
Instruct-ERIC is a pan-European research infrastructure in structural biology, making high-end technologies and methods available to all European researchers.
instruct-eric.org
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Jan 29
Are you working with circular dichroism (CD)? Check out the latest update to our ChiraKit tool, now with 10 tutorials to get you started! 🚀 Try it here: spc.embl-hamburg.de/app/chirakit
An abstract representation of what happens during a circular dichroism measurement. Left- and right-circularly polarized light passes through the sample. One of the components is more absorbed.
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Reposted by Osvaldo Burastero
cssbhamburg.bsky.social
Centre for Structural Systems Biology CSSB @cssbhamburg.bsky.social · Jan 9
The Sondermann group and collaborators @univofmaryland.bsky.social have identified a new family of bacterial enzymes termed diDNases. The research received a Breakthrough Article designation from Nucleic Acids Research.

Find out more: t1p.de/i07ua
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Dec 15
Journalist friend: you pay to publish your work? 😶
Me: yes, and we also review for free, and pay to read
Friend: are scientists okay?

Idk 😅
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osvalb.bsky.social
Osvaldo Burastero @osvalb.bsky.social · Dec 6
Apply now to learn about binding kinetics at the Institut Pasteur (April 2025) 🧪😁
klausenhauser.bsky.social
Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · Dec 6
📣 Do you like binding kinetics? Have already done some experiments and want to become more advanced? Join us for Kinetics 2025 @pasteur.fr ! Hands-on opportunity on instruments from almost all the vendors + Seminars + Data Fair discussion on data! #biophysics #kinetics www.mosbri.eu/training/adv...
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Reposted by Osvaldo Burastero
kmichie.bsky.social
Kate Michie @kmichie.bsky.social · Nov 17
So many people added to pack 1 this weekend we had to make pack 2. Makes sure you refresh for followers on pack one to see them all!
🧶🧬

go.bsky.app/DDetSBp
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