Mastouille

michaelI gather this is about reconstructing <a href="https://mastodon.social/tags/ribosome" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ribosome</a> <a href="https://mastodon.social/tags/assembly" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#assembly</a> in the <a href="https://mastodon.social/tags/nucleolus" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nucleolus</a> - the PR is a bit wild but may be worth looking at the paper in Nature. <a href="https://www.eurekalert.org/news-releases/1089618" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.eurekalert.org/news-releases/1089618</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.social/tags/nanoworld" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nanoworld</a> <a href="https://mastodon.social/tags/CellBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CellBiology</a> <a href="https://mastodon.social/tags/structuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralBiology</a>

Guillaume GaullierAn interesting use case of LLMs is as a conversational interface to some body of text, as a complement to other forms of navigation: from a table of content or index, via full-text search, or reading specific sections or even the whole text cover-to-cover.Of course the LLM can still make up nonsense, but this is a similar limitation to a full-text search leading to a section irrelevant to your current question if the search terms match too broadly. With any navigation method, eventually you need to read the material once you find the section you need.The Phenix documentation, papers, newsletters and tutorial videos have been fed to an LLM, so now we can navigate it as a conversation: <a href="https://phenix-online.org/version_docs/2.0-5725/reference/chatbot.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://phenix-online.org/version_docs/2.0-5725/reference/chatbot.html</a> A quick test trying to answer a question I knew the answer to suggests that it is working pretty well for sufficiently specific questions. This will likely be useful.<a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://fediscience.org/tags/crystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#crystallography</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

SBGridSBGrid's eLife paper received a citation in May from Joost Snijder from <a href="https://akademienl.social/@utrechtuniversity" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@utrechtuniversity</a> in <a href="https://fediscience.org/@eLife" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@eLife</a> Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry.Read more here: <a href="https://elifesciences.org/articles/101322?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=549&lea=24537&ctr=0&par=1&trk=a0NNv000000hGUXMA2" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://elifesciences.org/articles/101322?utm_source=AdaptiveMailer&utm_medium=email&utm_campaign=SBGrid%20Newsletters&org=1935&lvl=100&ite=549&lea=24537&ctr=0&par=1&trk=a0NNv000000hGUXMA2</a><a href="https://mstdn.science/tags/SBGrid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SBGrid</a> <a href="https://mstdn.science/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a>

michael30-May-2025 Uncovering a unique light-harvesting structure in marine <a href="https://mastodon.social/tags/algae" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#algae</a> Photosystem II–FCPII complex found in a marine alga could shape the future of artificial <a href="https://mastodon.social/tags/photosynthesis" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#photosynthesis</a> high-resolution analysis of a photosynthetic complex found in , Chrysotila roscoffensis. This marine alga belongs to the <a href="https://mastodon.social/tags/coccolithophore" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#coccolithophore</a> species known for producing calcium carbonate plates and fixing carbon at the ocean surface.<a href="https://www.eurekalert.org/news-releases/1085791" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.eurekalert.org/news-releases/1085791</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.social/tags/ecology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ecology</a> <a href="https://mastodon.social/tags/MarineBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MarineBiology</a> <a href="https://mastodon.social/tags/structuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralBiology</a>

Dave nλ=2dsinθHow we peer review structural data | Nature Structural & Molecular BiologyOf interest to <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://xtaldave.net/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a><a href="https://www.nature.com/articles/s41594-025-01567-9" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.nature.com/articles/s41594-025-01567-9</a>

Dave nλ=2dsinθNew Presidential executive order on proteins:All amino acids now to be right w̶i̶n̶g̶ handed.Leftist amino acids to be outlawed.(Also, Z-DNA is deemed to be Communist, and is prohibited.)Trans- and cis- peptide bonds to be banned.Non-binary amino acid Glycine to be banned.Proline is not a real amino acid and will be banned immediately.Phenylalanine looks and sounds a bit like Fentanyl, banned immediately.<a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://xtaldave.net/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://xtaldave.net/tags/PDB" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PDB</a>

michael26-Mar-2025 Remember <a href="https://mastodon.social/tags/ebola" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ebola</a>? Zooming in on the <a href="https://mastodon.social/tags/structure" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structure</a> of the still lethal <a href="https://mastodon.social/tags/virus" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#virus</a><a href="https://www.eurekalert.org/news-releases/1078261" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.eurekalert.org/news-releases/1078261</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.social/tags/structuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralBiology</a> <a href="https://mastodon.social/tags/protein" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#protein</a> <a href="https://mastodon.social/tags/capsid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#capsid</a>

François Ferron 🇪🇺 🔷️🔶️Our project for the SHADOC 🇪🇺 doctoral program has been selected. If you are interested to do an international <a href="https://fediscience.org/tags/PhD" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PhD</a> in structural virology <a href="https://bsky.brid.gy/r/https://bsky.app/profile/afmblab.bsky.social" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@afmblab.bsky.social</a> , the <a href="https://fediscience.org/tags/HellenicPasteurInstitute" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HellenicPasteurInstitute</a> and <a href="https://fediscience.org/tags/SynchrotronSoleil" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SynchrotronSoleil</a> please visit our proposal : <a href="https://schadoc.univ-amu.fr/en/call-candidates/health-well-being/garcom" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://schadoc.univ-amu.fr/en/call-candidates/health-well-being/garcom</a> ➡️ For application procedure please read carefully : <a href="https://schadoc.univ-amu.fr/en/call-candidates" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://schadoc.univ-amu.fr/en/call-candidates</a> ➡️ Call for candidates are open between March 10th and april 21st. <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://fediscience.org/tags/virology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#virology</a> <a href="https://fediscience.org/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> <a href="https://fediscience.org/tags/SXT" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SXT</a>

Dave nλ=2dsinθThe authors of this paper reversed the amino acid sequence of a nanobody and apparently expected it to function like the forward sequence.Yeah, no, that's not how proteins work. <a href="https://xtaldave.net/tags/Science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Science</a> @Strucbio <a href="https://xtaldave.net/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://pubpeer.com/publications/BB01ACDF81B4854C50ADF3C6B4DBBC" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://pubpeer.com/publications/BB01ACDF81B4854C50ADF3C6B4DBBC</a>

Prof Paula SalgadoNew <a href="https://mastodon.social/tags/PhDstudentship" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PhDstudentship</a> available in the <a href="https://mastodon.social/tags/Salgadolab" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Salgadolab</a> to study <a href="https://mastodon.social/tags/AMR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AMR</a> bacteria, <a href="https://mastodon.social/tags/Cdiff" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Cdiff</a> <a href="https://mastodon.social/tags/BugSlayer" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#BugSlayer</a> and develop your research skills in microbiology, <a href="https://mastodon.social/tags/structuralbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralbiology</a> and computational chemistry <a href="https://shorturl.at/trW35" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://shorturl.at/trW35</a> pls share and get in touch if you want to know more!

François Ferron 🇪🇺 🔷️🔶️There is an Associate Professor Position in <a href="https://fediscience.org/tags/Bioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bioinformatics</a> with a Focus on <a href="https://fediscience.org/tags/AI" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AI</a> Applications in Integrated <a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> available in our Institute in Marseilles (France) @afmblab.bsky.social <a href="https://bsky.brid.gy/r/https://bsky.app/profile/afmblab.bsky.social" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@afmblab.bsky.social</a> <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://a.gup.pe/u/bioinformatics" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@bioinformatics</a> The successful candidate will create his/her own team for developing and implementing innovative AI-based approaches to address key challenges in structural biology, including but not limited to: 1. Designing synthetic proteins with novel or enhanced enzymatic properties. 2. Developing synthetic protein or biomolecule binders for therapeutic or biotechnological applications. 3. Performing molecular docking of small molecules on therapeutic targets. 4. Modelling macromolecular complexes in silico.* Contact : For more information, please contact Juan Reguera, Unit Director, including a brief CV. Formal applications should include: • A detailed CV with a summary of past and present research and teaching activities. • A short description of research project and implementation plan. • A motivation letter.

Dave nλ=2dsinθThe name of my specialism is Macromolecular Crystallography. I refine models against crystallographic data that I have collected.Therefore I am in Macro Data Refinement I shall take no further questions.<a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://xtaldave.net/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a>

MCDuncanLabOk, Rab-biologists, GTP-G-S is unavailable for a couple of months. Does GMPPCP bind rabs well?Got any references?<a href="https://mstdn.social/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a>

Morten KjeldgaardAfter years of procrastinating I finally got around to publishing my Python module for reading mmCIF files. Check it out: <a href="https://pypi.org/project/mmcifbuddy/" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://pypi.org/project/mmcifbuddy/</a> and feel free to let me know how it goes! <a href="https://mastodon.online/tags/crystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#crystallography</a> <a href="https://mastodon.online/tags/structuralbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralbiology</a> <a href="https://mastodon.online/tags/mmcif" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#mmcif</a> cc: <a href="https://a.gup.pe/u/strucbio" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@strucbio</a> <a href="https://xtaldave.net/@xtaldave" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@xtaldave</a>

michaelmy features published in <a href="https://mastodon.social/tags/CurrentBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CurrentBiology</a> this year, issue 2: Reconstructing ancient <a href="https://mastodon.social/tags/OlfactorySensors" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#OlfactorySensors</a> may help solve the <a href="https://mastodon.social/tags/structures" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structures</a> of the modern ones <a href="https://proseandpassion.blogspot.com/2025/01/on-origins-of-smell.html" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://proseandpassion.blogspot.com/2025/01/on-origins-of-smell.html</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.social/tags/smell" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#smell</a> <a href="https://mastodon.social/tags/structuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralBiology</a> <a href="https://mastodon.social/tags/proteins" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#proteins</a> <a href="https://mastodon.social/tags/nanoworld" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nanoworld</a> <a href="https://mastodon.social/tags/alphaFold" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#alphaFold</a>

michael15-Jan-2025 Protein shapes can help untangle life’s ancient history A new way of merging genomic and structural data can help dive deep into evolutionary relationships<a href="https://www.eurekalert.org/news-releases/1070108" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.eurekalert.org/news-releases/1070108</a> <a href="https://mastodon.social/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.social/tags/proteins" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#proteins</a> <a href="https://mastodon.social/tags/nanoworld" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#nanoworld</a> <a href="https://mastodon.social/tags/evolution" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#evolution</a> <a href="https://mastodon.social/tags/structuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralBiology</a>

Stephen RoyleThis is pretty amazing. TMEM206 structure determined using a single HEK cell colony!"MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony”<a href="https://www.biorxiv.org/content/10.1101/2025.01.10.632437v1" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.biorxiv.org/content/10.1101/2025.01.10.632437v1</a><a href="https://biologists.social/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://biologists.social/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a>

jobRxivPostdoctoral Scholar-Structural Biology in Protein Dynamics Icahn School of Medicine at Mount SinaiJoin our lab as a <a href="https://mas.to/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://mas.to/tags/Postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Postdoc</a> to study proteins in <a href="https://mas.to/tags/Alzheimers" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Alzheimers</a> & <a href="https://mas.to/tags/Cancer" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Cancer</a> using <a href="https://mas.to/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> & <a href="https://mas.to/tags/XrayCrystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#XrayCrystallography</a> at Mount Sinai!See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai</a>... <a href="https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-scholar-structural-biology-in-protein-dynamics-2/?feed_id=89569" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-scholar-structural-biology-in-protein-dynamics-2/?feed_id=89569</a>

jobRxivPostdoctoral Scholar-Structural Biology in Protein Dynamics Icahn School of Medicine at Mount SinaiJoin our lab as a <a href="https://mas.to/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://mas.to/tags/Postdoc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Postdoc</a> to study proteins in <a href="https://mas.to/tags/Alzheimers" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Alzheimers</a> & <a href="https://mas.to/tags/Cancer" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Cancer</a> using <a href="https://mas.to/tags/CryoEM" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CryoEM</a> & <a href="https://mas.to/tags/XrayCrystallography" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#XrayCrystallography</a> at Mount Sinai!See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai</a>... <a href="https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-scholar-structural-biology-in-protein-dynamics-2/?feed_id=89072" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-scholar-structural-biology-in-protein-dynamics-2/?feed_id=89072</a>

Guillaume Gaullier<a href="https://fediscience.org/tags/DeepMind" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DeepMind</a> finally released the code of <a href="https://fediscience.org/tags/AlphaFold3" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AlphaFold3</a>! But with very restrictive conditions to use the model weights... And anyway, I wonder which academic lab has the hardware to run it, beside maybe David Baker's lab maybe...<a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBiology</a> <a href="https://fediscience.org/tags/StructuralBioinformatics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#StructuralBioinformatics</a>Announcement: <a href="https://doi.org/10.1038/d41586-024-03708-4" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1038/d41586-024-03708-4</a>Code: <a href="https://github.com/google-deepmind/alphafold3" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/google-deepmind/alphafold3</a>Hardware requirements: <a href="https://github.com/google-deepmind/alphafold3/blob/main/docs/performance.md#accelerator-hardware-requirements" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/google-deepmind/alphafold3/blob/main/docs/performance.md#accelerator-hardware-requirements</a>Form to request authorization to use the model weights: <a href="https://forms.gle/svvpY4u2jsHEwWYS6" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://forms.gle/svvpY4u2jsHEwWYS6</a>

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