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 ⬇️ journals.plos.org/ploscompbiol...

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...

🚨 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👇

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...

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/

Exploring the Potential of AlphaFold Distograms for Flexibility Assignment in Cryo-EM Maps www.biorxiv.org/content/10.1101/2025.07.25.666757v1 #cryoem

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...

Happy to share that our paper on Metric Ion Classification (MIC) is now published! www.nature.com/articles/s41...

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

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.

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

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

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

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.

Really cool work on diffusing structures into cryo-EM densities by Ellen Zhong et. al arxiv.org/html/2506.04... #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

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...

This has been a long journey, but it's now out in final form. @kjamali.bsky.social academic.oup.com/bioinformati...

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

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

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

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

📢 New preprint, lead by Alex Bronstein, @sankethvedula.bsky.social and colleagues: Guiding AlphaFold with experimental data. This approach generates conformational ensembles guided by NMR, X-ray (or whatever) data. I am thrilled to tackle lots of exciting problems with it! arxiv.org/abs/2502.09372

🧵 on our preprint: Zhang & Skolnick's TM score for comparing model of protein to experimental structures of same protein. The d_j are essentially the same as the aligned error in Alphafold. After any structure alignment, it's the displacement of model Calpha from experimental Calpha of residue j.

I have two open postdoctoral researcher positions in my group. I am looking for applicants with interest and expertise in computational structural biology and research software development. These positions are part of GANANA, a collaborative European/Indian project Check www.uu.nl/en/organisat...

Modeling ligands in cryo-EM with generative AI and density-guided simulations https://www.biorxiv.org/content/10.1101/2025.02.10.637508v1

Join us February 11th for the latest from our software webinar series & hear from João Rodrigues on Phenix/OPLS & GlideEM: Enabling cryoEM structures for drug discovery with the Schrodinger Suite. Tuesday, February 11, 2025 - 12:00pm ET Register here: https://buff.ly/36OEPwR #SBGrid #Webinars

Sometimes, the best discoveries start with curiosity! A few years ago, a motivated high school student joined the lab to explore lanthanide-induced shifts in metabolites. What happened next took us by surprise… 🧵👇

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹! www.biorxiv.org/content/10.1... 🧵👇 (1/n)

"Barrier", "bias", welp, there goes all funding for enhanced sampling methods.. seriously though, if true, this is plain stupid.

SFCalculator: connecting deep generative models and crystallography https://www.biorxiv.org/content/10.1101/2025.01.12.632630v1

Mass spec/proteomics chempostdoc in the Ferguson lab, UCSD, La Jolla, CA chemsky 🧪 ⚗️ jobrxiv.org/job/universi...

Exciting news! Our collaborative study reveals the molecular secrets of how #filoviruses, like #Ebola virus, interact with their #receptor and enter host cells. We also predict #bat species that could act as hosts for Ebola virus. Check it out: https://buff.ly/4akxlP1 1/10

Favourite paper of 2023 "Updated benchmarking of variant effect predictors using deep mutational scanning" by Livesey and Marsh. (1/4) www.embopress.org/doi/full/10....

Considering the large number of complexes we should have many more CAPRI targets! Please consider providing your complex as a a target for CAPRI - see capri-docking.org/contribute

Favourite paper of 2022 "End-to-end differentiable construction of molecular mechanics force fields" by Wang et al. (1/4) pubs.rsc.org/en/content/a...

Favourite paper of 2021 "Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting" by Thaler and Zavadlav. (1/4) www.nature.com/articles/s41...

Favourite paper of 2020 "Supervised Contrastive Learning" by Khosla et al. (1/4) proceedings.neurips.cc//paper/2020/...

Favourite paper of 2019 "Learning Protein Structure with a Differentiable Simulator" by Ingraham et al. (1/4) openreview.net/forum?id=Byg...

Honourable mention goes to Sorokina and Mushegian's paper on whether proteins can fold by themselves. You probably haven't heard of this one, but it will make you question everything you thought you knew. (4/4) biologydirect.biomedcentral.com/articles/10....

Favourite paper of 2018 "Developing a molecular dynamics force field for both folded and disordered protein states" by Robustelli et al. (1/4) www.pnas.org/doi/10.1073/...

Favourite paper of 2017 "Protein structure determination using metagenome sequence data" by Ovchinnikov et al. (1/4) www.science.org/doi/10.1126/...

Interested in building the future of open source ligand- and structure-based ML models for ADMET prediction? The ARPA-H funded OMSF (@omsf.bsky.social) OpenADMET project is hiring multiple positions to build ML models of ADMET properties and drive informative data collection! openadmet.org/jobs/

Favourite paper of 2016 "Design and synthesis of a minimal bacterial genome" by Hutchison et al. (1/3) www.science.org/doi/10.1126/...

Favourite paper of 2015 "Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field" by Wang et al. (1/4) pubs.acs.org/doi/10.1021/...

Favourite paper of 2014 "Building Force Fields: An Automatic, Systematic, and Reproducible Approach" by Wang et al. (1/4) pubs.acs.org/doi/10.1021/...

Favourite paper of 2013 "PeptideBuilder: A simple Python library to generate model peptides" by Tien et al. (1/4) peerj.com/articles/80

Favourite paper of 2012 "HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment" by Remmert et al. (1/4) www.nature.com/articles/nme...

The legendary EMBO Integrative Modeling Course is back! If you want to be in this picture in the 2025 edition, just go ahead and register at meetings.embo.org/event/25-bio... Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social