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jpglmrodrigues.bsky.social
João Rodrigues
@jpglmrodrigues.bsky.social
210 followers 56 following 30 posts
Computational Biologist and Team Lead at Schrodinger. Proteins & Python. Opinions are my own. https://joaor.eu
joaor.eu
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Reposted by João Rodrigues
bffo.bsky.social
BF Francis Ouellette @bffo.bsky.social · 13d
From @jdrakephd.bsky.social & @bahanbug.bsky.social in @plos.org #Computational #Biology | How to write a scientific paper in fifteen steps | #Education #Science 🧪 🔓 #GoodReadingForAll CC/ @ppalagi.bsky.social
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journals.plos.org/ploscompbiol...
How to write a scientific paper in fifteen steps
journals.plos.org
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Reposted by João Rodrigues
jchodera.bsky.social
John Chodera @jchodera.bsky.social · Sep 5
The next Bay Area COMP Together is Thu 2 Oct, featuring Jit Mukherjee (Gilead) describing the discovery of lencapavir and Jeff Blaney (Genentech) on lessons learned in 42 years of drug discovery!

www.linkedin.com/posts/comp-t...
Meet | COMP Together
Join us on Thursday October 2nd to connect with the computational chemistry community in the San Francisco Bay Area and hear about cool science! We will have time for networking, followed by 2 excit...
www.linkedin.com
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Reposted by João Rodrigues
busrasavas.bsky.social
Büşra Savaş @busrasavas.bsky.social · Jul 29
🚨 Super excited for our new preprint on flexibility cues in AlphaFold!

Together with @ezgikaraca.bsky.social and @aysebercinb.bsky.social, we found that distograms of AF2.3 and AF3 mirror MD sampling by predicting the extent of a novel conformational change! 🤯

For more👇
biorxiv-bioinfo.bsky.social
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 28
Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps https://www.biorxiv.org/content/10.1101/2025.07.25.666757v1
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Reposted by João Rodrigues
ezgikaraca.bsky.social
Ezgi Karaca @ezgikaraca.bsky.social · Jul 29
We just bumped into something very preliminary… but very exciting:

AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.

Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...
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Reposted by João Rodrigues
amjjbonvin.bsky.social
Alexandre Bonvin @amjjbonvin.bsky.social · Jul 29
A small reminder to all structural biologists around working on biomolecular complexes: please consider sharing your complexes as targets for CAPRI - AI has not solved all structure prediction problems and there are still challenges! See www.capri-docking.org/contribute/
CAPRI Docking
www.capri-docking.org
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Reposted by João Rodrigues
cryoempapers.bsky.social
cryoEM papers @cryoempapers.bsky.social · Jul 28
Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps www.biorxiv.org/content/10.1101/2025.07.25.666757v1 #cryoem
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Reposted by João Rodrigues
bioinfo.se
Arne Elofsson @bioinfo.se · Jul 12
A paper thar took too long to finish. We show that AlphaFold3 its clearly better than AlphaFold2 (and Boltz-1 and Chai-1) to predict the structure of antibody-Antigens, but only for cases with (har to detect) similarity in the training set.

www.biorxiv.org/content/10.1...
Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes
Motivation: AlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without co-evolutionary signals, such as host-pathogen and a...
www.biorxiv.org
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Reposted by João Rodrigues
biophysicsguy.bsky.social
Michael J. Robertson @biophysicsguy.bsky.social · Jul 7
Happy to share that our paper on Metric Ion Classification (MIC) is now published!

www.nature.com/articles/s41...
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Reposted by João Rodrigues
aktaguy.bsky.social
Ädam Ligeralde @aktaguy.bsky.social · Jun 28
Calling all structural biologists in the NYC metro area! The nysbdg.bsky.social is back for in-person events!

Register here 👉🏼 buff.ly/dGmJeau

I look forward to seeing you there! 😎

#structuralbiology #cyrstallography #cryoEM #NMR
#chromatography #proteinpurification #AKTAsystems
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Reposted by João Rodrigues
jgreener64.bsky.social
Joe Greener @jgreener64.bsky.social · Jun 16
Interested in a postdoc position combining computational protein design and molecular simulation? There is an open position in my group at the MRC-LMB in Cambridge, UK.

www.nature.com/naturecareer...

Feel free to message me with any questions.
Postdoctoral Scientist - Structural Studies - Dr Joe Greener - LMB 2633 - Cambridgeshire job with MRC Laboratory of Molecular Biology (LMB) | 12840475
Postdoctoral Scientist Salary £41,344 per annum  Fixed Term – 3 years MRC Laboratory of Molecular Biology, Cambridge, UK We are looking for a postd...
www.nature.com
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Reposted by João Rodrigues
machine.learning.bio
Christian Dallago @machine.learning.bio · Jun 15
With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp
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Reposted by João Rodrigues
ezgikaraca.bsky.social
Ezgi Karaca @ezgikaraca.bsky.social · Jun 11
Only a few days left to apply for our EMBO course with a great lineup of speakers and tutors! Please feel free to RT!

Course website: meetings.embo.org/event/25-bio...

Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social

Location: www.ibg.edu.tr
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 11
To put it simply, Europe funds education, the US funds research.
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 11
I get it. I was trying to make the point that Europe simply cannot make up for those cuts because it's a fundamentally different system.. in my opinion, making any type of comparisons is pointless.
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 11
And yet ~50% of postdocs in the US are foreigners :) I wouldn't compare different systems, built on societies with different sets of values. If Europe (et al) invests more as a result of US divestment, that's a net positive: more diversity of ideas, less concentration of IP, the list goes on..
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Reposted by João Rodrigues
matthieumontes.bsky.social
Matthieu Montes @matthieumontes.bsky.social · Jun 10
New paper out www.frontiersin.org/journals/bio...

VTX is available at github.com/VTX-Molecula...

@cg-martini.bsky.social @janstevens.bsky.social

@maximemaria.bsky.social @sguionni.bsky.social @pltc.bsky.social @qubit-pharma.bsky.social
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 10
The rendering style got me half expecting to see Goku and Vegeta pop up at any moment from behind a helix! Beautiful! Great job!!
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Reposted by João Rodrigues
lindorfflarsen.bsky.social
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jun 9
This paper combines two sort-of-crazy (in the best sense) approaches in cryoEM sample preparation:
(1) Native, soft-landing electrospray ion beam deposition, followed by (2) deposition of amorphous ice, and reheating and freezing by laser flash melting. Has potential for time-resolved studies.
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 9
Depending on where you'll be, try and look for local cycling/wheelers clubs. They're usually nice, organize rides, etc. A quick search for Boston shows www.crw.org which actually seems really nice!
Charles River Wheelers - HomePhoto Gallery
www.crw.org
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 8
Ah! Tomayto, tomahto 😜
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 7
Really cool work on diffusing structures into cryo-EM densities by Ellen Zhong et. al arxiv.org/html/2506.04...

#cryoem
Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data
arxiv.org
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jpglmrodrigues.bsky.social
João Rodrigues @jpglmrodrigues.bsky.social · Jun 6
New preprint from my colleagues at Schrödinger on blending ML methods with physics-based refinement and scoring to improve small molecule docking performance - and generalization - on several tasks for early stages of drug discovery. Link👇

www.biorxiv.org/content/10.1...

#chemsky
Several bar plots showing the improved performance and ability to generalize to unseen targets of Diffdock-Glide vs standard Diffdock.
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Reposted by João Rodrigues
amjjbonvin.bsky.social
Alexandre Bonvin @amjjbonvin.bsky.social · May 7
The manuscript describing the new modular version of HADDOCK is finally available as a preprint! The result of a team work over several years, supported by @bioexcelcoe.bsky.social @bijvoet-centre.bsky.social @esciencecenter.bsky.social - www.biorxiv.org/content/10.1...
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Reposted by João Rodrigues
jgreener64.bsky.social
Joe Greener @jgreener64.bsky.social · Apr 8
This has been a long journey, but it's now out in final form. @kjamali.bsky.social

academic.oup.com/bioinformati...
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Reposted by João Rodrigues
rolanddunbrack.bsky.social
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · Apr 7
Anybody know on TED (The Encyclopedia of Domains), what the domain-domain "Interaction score" is? I can't find it in the paper on or on the website. Example: kinase N and C terminal domains for EGFR have a score of 7.0:

ted.cathdb.info/uniprot/P00533
TED: The Encyclopedia of Domains
ted.cathdb.info
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