João Rodrigues
@jpglmrodrigues.bsky.social
Computational Biologist and Team Lead at Schrodinger. Proteins & Python. Opinions are my own.
https://joaor.eu
https://joaor.eu
Reposted by João Rodrigues
SBGrid's eLife paper received a citation in September from @jpglmrodrigues.bsky.social from Schrödinger, Inc. in FEBS Letters: Towards better structural models from cryo-electron microscopy data with physics-based methods.
Read more here: buff.ly/xqvFJ8g
#SBGrid #ScienceMatters
Read more here: buff.ly/xqvFJ8g
#SBGrid #ScienceMatters
Towards better structural models from cryo-electron microscopy data with physics-based methods - PubMed
Cryo-electron microscopy can now routinely deliver atomic resolution structures for a variety of biological systems. The relevance and value of these structures are directly related to their ability…
buff.ly
October 28, 2025 at 4:07 PM
SBGrid's eLife paper received a citation in September from @jpglmrodrigues.bsky.social from Schrödinger, Inc. in FEBS Letters: Towards better structural models from cryo-electron microscopy data with physics-based methods.
Read more here: buff.ly/xqvFJ8g
#SBGrid #ScienceMatters
Read more here: buff.ly/xqvFJ8g
#SBGrid #ScienceMatters
Reposted by João Rodrigues
New Title Alert: ARCTIC-3D- a software for data-mining and clustering of protein interface information.
Learn more here: buff.ly/IbbwP2N
#SBGridSoftware #StructuralBiology #SBGrid
Learn more here: buff.ly/IbbwP2N
#SBGridSoftware #StructuralBiology #SBGrid
Arctic3D Webserver
Home
buff.ly
October 10, 2025 at 4:07 PM
New Title Alert: ARCTIC-3D- a software for data-mining and clustering of protein interface information.
Learn more here: buff.ly/IbbwP2N
#SBGridSoftware #StructuralBiology #SBGrid
Learn more here: buff.ly/IbbwP2N
#SBGridSoftware #StructuralBiology #SBGrid
Reposted by João Rodrigues
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...
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journals.plos.org/ploscompbiol...
How to write a scientific paper in fifteen steps
journals.plos.org
September 25, 2025 at 12:29 PM
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...
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journals.plos.org/ploscompbiol...
Reposted by João Rodrigues
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...
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
September 5, 2025 at 3:34 AM
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...
www.linkedin.com/posts/comp-t...
Reposted by João Rodrigues
🚨 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👇
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👇
Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps https://www.biorxiv.org/content/10.1101/2025.07.25.666757v1
July 29, 2025 at 12:52 PM
🚨 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👇
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👇
Reposted by João Rodrigues
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...
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...
July 29, 2025 at 1:01 PM
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...
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...
Reposted by João Rodrigues
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
July 29, 2025 at 6:26 AM
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/
Reposted by João Rodrigues
Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps www.biorxiv.org/content/10.1101/2025.07.25.666757v1 #cryoem
July 28, 2025 at 6:40 PM
Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps www.biorxiv.org/content/10.1101/2025.07.25.666757v1 #cryoem
Reposted by João Rodrigues
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...
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
July 12, 2025 at 2:13 AM
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...
www.biorxiv.org/content/10.1...
Reposted by João Rodrigues
Happy to share that our paper on Metric Ion Classification (MIC) is now published!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
July 7, 2025 at 2:38 PM
Happy to share that our paper on Metric Ion Classification (MIC) is now published!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by João Rodrigues
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
Register here 👉🏼 buff.ly/dGmJeau
I look forward to seeing you there! 😎
#structuralbiology #cyrstallography #cryoEM #NMR
#chromatography #proteinpurification #AKTAsystems
June 28, 2025 at 3:54 PM
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
Register here 👉🏼 buff.ly/dGmJeau
I look forward to seeing you there! 😎
#structuralbiology #cyrstallography #cryoEM #NMR
#chromatography #proteinpurification #AKTAsystems
Reposted by João Rodrigues
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.
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
June 16, 2025 at 10:47 AM
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.
www.nature.com/naturecareer...
Feel free to message me with any questions.
Reposted by João Rodrigues
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
June 15, 2025 at 11:30 AM
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
Reposted by João Rodrigues
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
Course website: meetings.embo.org/event/25-bio...
Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social
Location: www.ibg.edu.tr
June 11, 2025 at 8:48 AM
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
Course website: meetings.embo.org/event/25-bio...
Organizers: myself, @amjjbonvin.bsky.social @bioinfo.se @lindorfflarsen.bsky.social
Location: www.ibg.edu.tr
Reposted by João Rodrigues
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
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
June 10, 2025 at 7:43 AM
Reposted by João Rodrigues
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.
(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.
June 9, 2025 at 6:43 AM
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.
(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.
Really cool work on diffusing structures into cryo-EM densities by Ellen Zhong et. al arxiv.org/html/2506.04...
#cryoem
#cryoem
Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data
arxiv.org
June 7, 2025 at 5:52 PM
Really cool work on diffusing structures into cryo-EM densities by Ellen Zhong et. al arxiv.org/html/2506.04...
#cryoem
#cryoem
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
www.biorxiv.org/content/10.1...
#chemsky
June 6, 2025 at 4:45 PM
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
www.biorxiv.org/content/10.1...
#chemsky
Reposted by João Rodrigues
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...
May 7, 2025 at 3:50 PM
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...
Reposted by João Rodrigues
This has been a long journey, but it's now out in final form. @kjamali.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
April 8, 2025 at 1:47 PM
This has been a long journey, but it's now out in final form. @kjamali.bsky.social
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by João Rodrigues
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.cathdb.info/uniprot/P00533
TED: The Encyclopedia of Domains
ted.cathdb.info
April 7, 2025 at 10:52 PM
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.cathdb.info/uniprot/P00533
My team at Schrödinger is looking for 2 interns to join us in NYC for 3 months this summer!
If you are comfortable writing Python, know (even a little!) about protein structure, and can work in the US, feel free to reach out!
Check the kind of work we do 👇
tinyurl.com/43j57uww
If you are comfortable writing Python, know (even a little!) about protein structure, and can work in the US, feel free to reach out!
Check the kind of work we do 👇
tinyurl.com/43j57uww
Enabling cryoEM structures for drug discovery with the Schrödinger Suite - Schrödinger
In drug discovery, the relevance and value of protein structures is directly related to their ability to rationally optimize molecular properties.
tinyurl.com
March 15, 2025 at 2:24 AM
My team at Schrödinger is looking for 2 interns to join us in NYC for 3 months this summer!
If you are comfortable writing Python, know (even a little!) about protein structure, and can work in the US, feel free to reach out!
Check the kind of work we do 👇
tinyurl.com/43j57uww
If you are comfortable writing Python, know (even a little!) about protein structure, and can work in the US, feel free to reach out!
Check the kind of work we do 👇
tinyurl.com/43j57uww
Reposted by João Rodrigues
Google Summer of Code projects are available this year to improve molecular simulation in Molly.jl.
Feel free to ask me any questions.
julialang.org/jsoc
Feel free to ask me any questions.
julialang.org/jsoc
Hear from some of our past GSoC contributors
julialang.org
March 13, 2025 at 11:01 AM
Google Summer of Code projects are available this year to improve molecular simulation in Molly.jl.
Feel free to ask me any questions.
julialang.org/jsoc
Feel free to ask me any questions.
julialang.org/jsoc
Many thanks to @sbgrid.bsky.social for inviting us to talk about our structure refinement tools for #cryoem - better structures enable better predictions. It was a pleasure to share the work of many talented group members over the years!
youtu.be/g11qEvSmTLs
youtu.be/g11qEvSmTLs
Schrödinger
YouTube video by SBGrid Consortium
youtu.be
March 4, 2025 at 9:30 PM
Many thanks to @sbgrid.bsky.social for inviting us to talk about our structure refinement tools for #cryoem - better structures enable better predictions. It was a pleasure to share the work of many talented group members over the years!
youtu.be/g11qEvSmTLs
youtu.be/g11qEvSmTLs
Reposted by João Rodrigues
