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AlphaFold3 is out (and closed source ๐คฏ๐ )! So โฆ how well does it do on peptide-protein complexes?
A continuing thread as we run predictions...
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Ora Furman Lab ๐
418 posts
Ora Furman Lab ๐
@FurmanLab
Structural basis of peptide-mediated protein communication and function @HebrewU Member of @RosettaCommons. Tweets by lab members. ๐ฆ https://t.co/UMEreURWke ๐ฆ
Jerusalem, Israel ๊ฐ์
์ผ Aฤustos 2020
479 ํ๋ก์1.2K ํ๋ก์
๐ฆ Find us also on bluesky ๐ฆ
furmanlab.bsky.social
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If you want to integrate it in your own AF3 installation, check the 3 files which only need a slight modification (model.py, confidences.py and confidence_types.py):
github.com/Kuhlman-Lab/alโฆ
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๐จ actifpTM is now in AF3 ๐จ
Since our new metric, actifpTM, was determined to be the best for predicting success in designed proteins refolded by AF2 (biorxiv.org/content/10.110โฆ by @TimothyPJenkins), we made it available also in AF3!
Ora Furman Lab ๐@FurmanLab
Our work on refining AlphaFold2โs ipTM has been accepted for publication in Bioinformatics @OxfordJournals We have been questioning why ipTM worsens when docking peptides with disordered flanking regions, and modified the calculation to remove this effect. Letโs dive in! ๐
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
๐จThe Bits to Binders Competition has concluded!๐งฌ
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
1/13 ๐งต Today, Bindcraft was published in @Nature , one of the most famous AIs in biology for designing proteinโprotein interactions (PPI). In my opinion. Bindcraft represents one of the most important advances in the postโAlphaFold2 era.
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
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This was an amazing collaboration with the @lab_wiener and @RouvinskiLab - thank you! ๐
Graphical abstract below โฌ๏ธ
#SARSCoV2 #COVID19 #Virology #CellReports #ComplementSystem #Immunology
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๐ก Heparin analogs (like Enoxaparin) block NP surface binding, preventing immune complex formation and rescuing cells from complement attack.
A possible path to reduce immunopathology.
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๐จExcited to share our new work in Cell Reports!
We reveal how SARS-CoV-2 nucleocapsid protein (NP) directs complement attack on uninfected cells, a surprising immune evasion twist.
๐ cell.com/cell-reports/fโฆ
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
Our paper is out on biorxiv! Very excited to share our results - we find signal peptides might be structurally important for quite a few protein isoforms. Full thread soon!
bioRxiv Bioinfo@biorxiv_bioinfo
Signal peptides as potential structural modulators of human splice isoforms biorxiv.org/content/10.110โฆ #biorxiv_bioinfo
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
If you missed out on Sarel Fleishman's extraordinary talk last night, have no fear - you can check out the recording ๐
youtu.be/2aaWh8yVq8U
YouTube
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Starts in 10 minutes! This will be exciting, join us!
PMC Protein Modules Community@PMC_modularity
Join us at 6pm CET May 12 for the next seminar in our series with Prof. Tony Hunter (@salkinstitute) and Dr. Jesรบs Alvardo Valverde (@imbmainz). Register to attend:ย tinyurl.com/PMCseminar2ย (1/2)
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
Remember to tune in at 6pm CET May 12 for the next seminar in our series with Prof. Tony Hunter (@salkinstitute) and Dr. Jesรบs Alvarado-Valverde (@imbmainz).
Register to attend:ย
tinyurl.com/PMCseminar2
PMC Protein Modules Community@PMC_modularity
Join us at 6pm CET May 12 for the next seminar in our series with Prof. Tony Hunter (@salkinstitute) and Dr. Jesรบs Alvardo Valverde (@imbmainz). Register to attend:ย tinyurl.com/PMCseminar2ย (1/2)
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The work is led by Manoj Kumar and Sayanika Banerjee. ๐
Check out the full story: doi.org/10.1038/s41467โฆ
#StructuralBiology #Ufmylation #NatureComms
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Excited to share new work from our lab in Nature Communications! ๐
We uncover how UFC1 โ an E2 enzyme without the classic HPN motif โ stabilizes critical oxyanion intermediates.
๐ doi.org/10.1038/s41467โฆ
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Ora Furman Lab ๐ ๋ฆฌํธ์ํจ
Either if you attended or wanted but could not - please tell us how it works for you!
PMC Protein Modules Community@PMC_modularity
Thanks to everyone who has attended the PMC seminars! We have decided to review the timing of the seminar series. If you have any thoughts about the timing of the seminars (currently 6-7pm CET every 2nd Mon of the month), please fill out this form: forms.gle/VZkU2fWkswxYbrโฆ
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