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#structuralbiology

2 messages2 participants0 message aujourd’hui

An 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: phenix-online.org/version_docs
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.

phenix-online.orgUsing the Phenix chatbot assistant

New 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.

@strucbio #StructuralBiology #PDB

Our project for the SHADOC 🇪🇺 doctoral program has been selected. If you are interested to do an international #PhD in structural virology @afmblab.bsky.social , the #HellenicPasteurInstitute and #SynchrotronSoleil please visit our proposal : schadoc.univ-amu.fr/en/call-ca
➡️ For application procedure please read carefully : schadoc.univ-amu.fr/en/call-ca
➡️ Call for candidates are open between March 10th and april 21st.
@strucbio #StructuralBiology #virology #CryoEM #SXT

schadoc.univ-amu.frGARCOM | SCHADOC

There is an Associate Professor Position in #Bioinformatics with a Focus on #AI Applications in Integrated #StructuralBiology available in our Institute in Marseilles (France) @afmblab.bsky.social
@afmblab.bsky.social
@strucbio @bioinformatics

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.

This 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”

biorxiv.org/content/10.1101/20

bioRxiv · MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colonySingle particle cryo-EM enables reconstructing near-atomic or even atomic resolution 3D maps of proteins by visualizing thousands to a few million purified protein particles embedded in nanometer-thick vitreous ice. This corresponds to picograms of purified protein, which can potentially be isolated from a few thousand cells. Hence, cryo-EM holds the potential of one of the most sensitive analytical methods that deliver a high-resolution protein structure as a readout. In practice, more than a million times more starting biological material is required to prepare cryo-EM grids. To close the gap, we developed a micro isolation (MISO) method that combines microfluidics-based protein purification with cryo-EM grid preparation. We validated the method on soluble bacterial and eukaryotic membrane proteins. We showed that MISO enables protein structure determination starting from below one microgram of a target protein and going from cells to cryo-EM grids within a few hours. This scales down the purification by a factor of a few hundred to a few thousand and opens possibilities for the structural characterization of hitherto inaccessible proteins. ### Competing Interest Statement G.E. and R.G.E are inventors on the patent application WO WO2023/232662/A1 disclosing the MISO instrument and chip design filed by VIB and VUB.

#DeepMind finally released the code of #AlphaFold3! 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...

#StructuralBiology #StructuralBioinformatics

Announcement: doi.org/10.1038/d41586-024-037

Code: github.com/google-deepmind/alp

Hardware requirements: github.com/google-deepmind/alp

Form to request authorization to use the model weights: forms.gle/svvpY4u2jsHEwWYS6

"AI protein-prediction tool AlphaFold3 is now open source" ... almost.

"Anyone can now download the AlphaFold3 software code and use it non-commercially. But for now, only scientists with an academic affiliation can access the training weights on request"

Stop gatekeeping you priiiiickssss.

#StructuralBiology @strucbio #Alphafold

nature.com/articles/d41586-024

www.nature.comAI protein-prediction tool AlphaFold3 is now open sourceThe code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.