jankosinski.bsky.social @jankosinski.bsky.social · 22/08/2025⏰ URGENT! ⏰ Into structural modeling, design, integration with experiments, evolution, or platforms? Join our conference, share your work, and see what’s hot! Only 4 days left to submit your abstract! 👇 010
Reposted by @jankosinski.bsky.socialEMBL Events @events.embl.org · 24/07/2025Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️ s.embl.org/csb25-01-bl 053
jankosinski.bsky.social @jankosinski.bsky.social · 28/07/2025One month remaining to register for our conference! Have a look at the outstanding speakers and programme, and use the link to join the 2nd edition of the Computational Structural Biology Conference in Heidelberg! 072
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025Check out HMFF and Mosaic on GitHub: (7/n) 🔗 github.com/KosinskiLab/... 010
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025HMFF comes with Mosaic, a software ecosystem for membrane segmentation, refinement, HMFF simulations, and morphometrics. (6/n) 🔗https://github.com/KosinskiLab/mosaic 110
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025For example, it allows building models like this filamentous influenza A virion ⬇️ (5/n) 100
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025HMFF aids in on-membrane particle picking, supports multiscale modeling, and allows backmapping to atomic detail (4/n) 100
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025This enables physically realistic and complete membrane models of cells, organelles, and viruses, consistent with experimental data (3/n) 100
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025Helfrich Monte Carlo Flexible Fitting (HMFF) optimizes membrane models directly in electron microscopy densities (2/n) 100
jankosinski.bsky.social @jankosinski.bsky.social · 30/05/2025New method toward modeling cells and viruses! HMFF enables integrative membrane modeling and simulation guided by electron microscopy data. Created by Valentin Maurer and Marc Siggel @embl.org @cssbhamburg.bsky.social, in collaboration with @WPezeshkian lab (1/n) www.biorxiv.org/content/10.1... 12710
Reposted by @jankosinski.bsky.socialEva Kowalinski @kowaeva.bsky.social · 16/04/2025Are you a postdoc ready for transition to an independent position? You connect infection biology with cutting-edge structural biology or multimodal imaging? Are you aware of such a colleague? I am seeking speakers for "The Next Generation in Infection Biology" microsymposium on June 6 2025. 078
Reposted by @jankosinski.bsky.socialCentre for Structural Systems Biology CSSB @cssbhamburg.bsky.social · 04/04/202528 children spent the day at CSSB for Girls' and Boys' Day yesterday! The kids built microscopes, conducted chemistry and chromatography experiments, tried VR goggles and much more. @carobarisch.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social @topf-lab.bsky.social 092
jankosinski.bsky.social @jankosinski.bsky.social · 29/03/2025Great work led by our PhD student Iuliia Kotova in collaboration with Fan Liu @fan-liu.bsky.social, Boris Bogdanow, Lars Mühlberg, and Olivier Duss @olivierduss.bsky.social and Guelsah Gabriel labs. Structural analysis by our PhD student Konstantin Gilep. www.biorxiv.org/content/10.1...biorxiv.orgSnapshot of in-cell protein contact sites reveals new host factors and hijacking of paraspeckles during influenza A virus infectionInfluenza A virus (IAV) exploits the host cellular machinery to facilitate its replication, yet many host-IAV interactions remain unexplored in the cellular context. Detailed information about interac... 061
jankosinski.bsky.social @jankosinski.bsky.social · 29/03/2025We captured a snapshot of in-cell protein contact sites during influenza A virus infection. In-cell crosslinking, AlphaFold modeling, and functional follow-ups revealed new host factors and mechanisms. A step toward modeling the infected cell. 2323
jankosinski.bsky.social @jankosinski.bsky.social · 28/03/2025Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out. #chatgpt4o 010
jankosinski.bsky.social @jankosinski.bsky.social · 27/03/2025Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations. 151
Reposted by @jankosinski.bsky.socialEMBL Events @events.embl.org · 24/02/2025Join us in Heidelberg for the 2nd edition of #EMBOComp3D! 🧬 Explore cutting-edge AI-driven innovations and classical methods in biomolecular research, new sessions on drug design, and make contacts during the job fair. Submit your abstract by 26 Aug 👉 s.embl.org/csb25-01-bl 0208
Reposted by @jankosinski.bsky.socialEMBL Events @events.embl.org · 06/02/2025⏰ You have until 3 March to submit your abstract and be part of #EESInfection ➡️ s.embl.org/ees25-04-bl 🦠 🍄 This symposium will bring together researchers working on different pathogens and pave the way for new strategies to overcome current challenges in the treatment of infections 💡 01513
jankosinski.bsky.social @jankosinski.bsky.social · 09/02/2025"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design." 020
Reposted by @jankosinski.bsky.socialProtein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 17/01/2025PDB-IHM (formerly PDB-Dev) is for integrative structures. Intergrative structures = from multiple experimental & computational methods. Since mid-2024 assigned PDB ids & DOIs. Access via wwPDB archive or PDB-IHM - pdb-ihm.org 👉 www.wwpdb.org/news/news?year=2025#6… 084
Reposted by @jankosinski.bsky.socialEzgi Karaca @ezgikaraca.bsky.social · 02/01/2025The 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 04130
jankosinski.bsky.social @jankosinski.bsky.social · 08/12/2024"Challenges along the way, but it worked out in the end" youtu.be/HnT1VWzdFWc?...youtu.be2024 Nobel Prize lectures in chemistry | David Baker, Demis Hassabis and John JumperYouTube video by Nobel Prize 010
jankosinski.bsky.social @jankosinski.bsky.social · 08/12/2024Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉 040
Reposted by @jankosinski.bsky.socialMax Bonomi @bonomimax.bsky.social · 06/12/2024Do you want to work at the interface of molecular simulations, structural biology experiments and #AI? Come to Paris for a PhD at @pasteur.fr 1 PhD position is available in our lab funded by ERC_Research. Please repost!! #compchem #compbio Info 👇 research.pasteur.fr/b/15Hrresearch.pasteur.frOne PhD thesis in integrative structural biology | Research - Institut Pasteur 15340
Reposted by @jankosinski.bsky.socialArne Elofsson @handle.invalid · 03/12/2024Conclusion for ligand session in #casp16, without a template methods fail 1175
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024Does anyone know of published test cases I can use to evaluate the approach? Ideally, the test case would feature a structure published after 30 September 2021, fail with AlphaFold3, and include real crosslinking data. 010
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024We still need to see how it generalizes and compares to other tools, but it feels promising, also from looking at results in our running projects! 000
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024By the way, seeds are your friends when running AlphaFold 3. I use at least 20 by default. 061
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024... and database of precalculated input features (MSA+templates) for 12 model organisms. I will post more details about these features later! (2/2) 000
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024Among the new features are new syntax, more automation, ModelCIF support, multimeric templates, input and output data storage management, support for crosslink-based modeling using Rappsilber lab's AlphaLink2, flexible backend system, and ... (1/2) 100
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024By amazing team Dmitry Molodenskiy, Valentin Maurer, Dingquan Yu, Grzegorz Chojnowski @gchojnowski.bsky.social, Konstantin Gilep with help from @torstenschwede.bsky.social group. 110
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024We have released version 2 of AlphaPulldown - a general pipeline for high-throughput structural modeling! Software: github.com/KosinskiLab/... Preprint: biorxiv.org/content/10.1... 1309
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024Proof-of-concept implementation: github.com/KosinskiLab/... Technical report: www.biorxiv.org/content/10.1...biorxiv.orgImproving AlphaFold 3 structural modeling by incorporating explicit crosslinksAlphaFold 3 has significantly advanced the modeling of macromolecular structures, including proteins, DNA, RNA, and their interactions with small molecules or post-translational modifications. However... 170
jankosinski.bsky.social @jankosinski.bsky.social · 04/12/2024Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea. 310323
jankosinski.bsky.social @jankosinski.bsky.social · 03/12/2024Thanks! Usalign command line worked for me for the global TM-score and it has nice chain matching procedure. DockQ - ah yes, of course! Do you or other know a program to calculate also 1) interface TM score (can't see it in Usalign) 2) fnat ? 100
Reposted by @jankosinski.bsky.socialArne Elofsson @handle.invalid · 02/12/2024Finally on board the Flight towards #casp16. If you want to see my talk you can find it here m.youtube.com/watch?v=w1fG...m.youtube.comCASP16 Lecture - ElofssonYouTube video by Introduction to Bioinformatics by Arne Elofsson at Stockholm University 0263
jankosinski.bsky.social @jankosinski.bsky.social · 02/12/2024#casp16 @arneelof.bsky.social @amjjbonvin.bsky.social what is the current state-of-the-art measure for reporting the quality of protein-protein docking models? sequence-dependent interface TM-score? Fnat? I guess not interface RMSD? What tool would you recommend to calculate all of them? 330
Reposted by @jankosinski.bsky.socialKonstantin Korotkov @korotkov-lab.bsky.social · 01/12/2024Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold. #CASP16 1206
Reposted by @jankosinski.bsky.socialArne Elofsson @handle.invalid · 28/11/2024#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .predictioncenter.org 24118
Reposted by @jankosinski.bsky.socialArjen Jakobi @cryotud.bsky.social · 18/11/2024Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning! Many of our speakers/tutors are here: @moalquraishi.bsky.social @sykhalid.bsky.social @ezgikaraca.bsky.social @amjjbonvin.bsky.social @gchojnowski.bsky.social @drmelissagraewert.bsky.social 0288
Reposted by @jankosinski.bsky.socialAndy Tseng @andytseng.bsky.social · 14/11/2024UPDATE: Nature.com has issued a correction: “Correction 14 November 2024: An earlier version of this article stated that AlphaFold3 is now ‘open source’. This is not the case, as weights for the model can only be accessed upon request, and the code can only be used for non-commercial applications.”nature.comAI protein-prediction tool AlphaFold3 is now more openThe code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics. 0208
jankosinski.bsky.social @jankosinski.bsky.social · 15/11/2024Hello, I am Jan, and I like molecules and other molecules. Where is a bookmark post button? 010
