Peter Rose @peterwrose
Director, Structural Bioinformatics Laboratory, San Diego Supercomputer Center, UC San Diego github.com/sbl-sdsc San Diego, CA Joined May 2016-
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Today's the day: PDB no longer has 3-character chemical component IDs for incoming depositions. 1st structure with a 5-character CCD has been deposited. Details at wwPDB: PDB Entries w/Novel Ligands Now Distributed Only in PDBx/mmCIF & PDBML File Formats wwpdb.org/news/news?year…
Very excited to share RoseTTAFold All-Atom and RFdiffusion All-Atom, methods for structure prediction and design of biomolecular assemblies! biorxiv.org/content/10.110… 1/n
ChatGPT can now see, hear, and speak. Rolling out over next two weeks, Plus users will be able to have voice conversations with ChatGPT (iOS & Android) and to include images in conversations (all platforms). openai.com/blog/chatgpt-c…
617M Protein model: ESM Metagenomic Atlas: The first view of the ‘dark matter’ of the protein universe ai.facebook.com/blog/protein-f…
LLMs can also learn the language of Covid-19. Here, @BioNTech_Group and @instadeepai built a model to predict high-risk Covid-19 variants far before the WHO designated them as variants. The model ingests viral spike protein sequences and predicts their immune escape and fitness.
🪩The @stateofaireport 2022 is live!🪩 In its 5th year, the #stateofai report condenses what you *need* to know in AI research, industry, safety, and politics. This open-access report is our contribution to the AI ecosystem. Here's my director's cut 🧵: stateof.ai
Today in partnership with @emblebi, we’re releasing predicted structures for nearly all catalogued proteins known to science, which will expand the #AlphaFold database by over 200x - from nearly 1 million to 200+ million structures: dpmd.ai/AF-22-TW 1/
ColabFold makes folding with #AlphaFold & #RoseTTAfold accessible to everyone. Our MSA server processed >1.6 million requests to date. We thank the community for all the help to improve Colabfold. Now published @naturemethods 📄 nature.com/articles/s4159…
After the enormous jump in accuracy of protein structure prediction by deep learning #AI methods: are models good enough to predict protein ligand complexes e.g. for #DrugDesign? #CASP15 pilot experiment open for registration, first targets coming soon: predictioncenter.org/news.cgi#421
@MelaxTech & SDSC secure a $300,000 Phase I @NIH #SBIR contract focused on the development and enhancement of innovative user-focused informatic tools for basic and clinical research on infectious, immune and allergic diseases. Read the full story: sdsc.edu/News%20Items/P… #AI
The #AlphaFold database has doubled in size today & now includes more than 800,000 structures. This is just one more step towards releasing 100+ million protein structures over the next year, that will cover almost every sequenced protein known to science!!
The #AlphaFold database has doubled in size today & now includes more than 800,000 structures. This is just one more step towards releasing 100+ million protein structures over the next year, that will cover almost every sequenced protein known to science!!
Proud of our latest work applying AI to Quantum Chemistry published in @ScienceMagazine! The properties of materials largely depend on their electrons. We introduce a new SOTA functional DM21 (open-sourced) that can accurately model many types of molecules deepmind.com/blog/article/S…
We’ve created calculator that aggregates deep mutational scanning data to estimate how mutations to #SARSCoV2 RBD affect recognition by human polyclonal antibodies. The calculator emphasizes extensive antigenic change in #Omicron variant. jbloomlab.github.io/RBD_escape_cal… (1/n)
Congrats, Frank!
End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman biorxiv.org/content/10.110… A fun collaboration with Samantha Petti, Nicholas Bhattacharya, @proteinrosh, @JustasDauparas, @countablyfinite, @keitokiddo, @srush_nlp & @pkoo562 (1/8)
Protein complex prediction with AlphaFold-Multimer biorxiv.org/cgi/content/sh… #bioRxiv
As you can see in this comparison between the #AlphaFold2 model (blue) and the experimental crystal structure (red), the prediction was nearly perfect, with a RMSD of only 0.4 A over 84 of 107 C-alpha atoms. Amazing accuracy! 4/6
John Chodera (he/him) @jchodera
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41 Followers 120 Following PhD student in Computational Biology and Bioinformatics at Duke Universitymars huang @MarsScHuang
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9K Followers 8K Following Changing drug discovery one ratio of partition functions at a time. Heading up antiviral discovery for pandemics: https://t.co/uN4XpX1mjt https://t.co/YAg9PBYuBlUC San Diego Research.. @ResearchUCSD
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1.3M Followers 153 Following Explore #NSFfunded research that is transforming the world. Social media policy: https://t.co/IRuZ2l1oLWPyTorch @PyTorch
380K Followers 77 Following Tensors and neural networks in Python with strong hardware acceleration. PyTorch is an open source project at the Linux Foundation. #PyTorchFoundationOpen Molecular Softwa.. @openmsf
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14K Followers 1 Following A research workshop on large language model gathering 1000+ researchers around the world Follow the training of the 176B multilingual model live @BigScienceLLMAli Madani @thisismadani
6K Followers 1K Following Founder & CEO of Profluent (https://t.co/GpoVdKW1zQ, we're hiring!). AI+Biology to cure disease. Berkeley PhD. formerly Research @ Salesforce AI.IDG Pharos @idg_pharos
271 Followers 128 Following A web interface enabling access to the Illuminating the Druggable Genome (IDG) knowledgebase. https://t.co/B6fQsJxbrtTorsten Schwede @TorstenSchwede
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4K Followers 66 Following a community of computational protein engineers and modelers from both academia and industry an @openmsf project organized by @bahl_lab @nickpolizzi_ @sokryptonMinkyung Baek @minkbaek
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5K Followers 3K Following executive director @carbonplanorg. previously: neuroscience and computational biology. open source, open science, collaboration. (he/him)Jake VanderPlas @jakevdp
42K Followers 438 Following Coffee and Python, preferably in that order. Dad of two girls; once-astronomer; author of @pydatasci, working on JAX and Altair. https://t.co/yKeqcBuFtAI got tenure at Seoul National University! Starting off with as a first-gen with a lower secondary education (Hauptschule) in Germany makes this very meaningful to me. I am grateful for all that supported and believed in me. Excited for what lies ahead!
Congrats, @KnightLabNews!!! Very well-deserved!
Congratulations to @UCSanDiego Professor Rob Knight, an int'l leader in the study of the roles microbes play in human health and the functioning of ecosystems, who has been elected to @theNAEng! This is the highest professional recognition for engineers: today.ucsd.edu/story/renowned…
On behalf of my coauthors, I'm psyched to announce the open access publication of our paper (with code) "Thompson Sampling - An Efficient Method for Searching Ultralarge Synthesis on Demand Databases" in JCIM. pubs.acs.org/doi/10.1021/ac…
@yvazirabad @tomashelikar @uni_tue My alma mater, the Martin Luther University (@UniHalle) will promote me as a full professor for “Data Analytics and Bioinformatics” in February next year. That is where I came from to Tübingen exactly 18 years earlier by the day.
My first close-up shots of the new eruption on Reykjanes Peninsula which began a few hours ago (December 19th, 2023). © Hörður Kristleifsson - @h0rdur
Today's the day: PDB no longer has 3-character chemical component IDs for incoming depositions. 1st structure with a 5-character CCD has been deposited. Details at wwPDB: PDB Entries w/Novel Ligands Now Distributed Only in PDBx/mmCIF & PDBML File Formats wwpdb.org/news/news?year…
Curious to see how the new PDB identifier, with 5-characters instead of 4, will impact bioinformatics pipelines. This might be a "millennium bug" moment in structure bioinformatics.
Today's the day: PDB no longer has 3-character chemical component IDs for incoming depositions. 1st structure with a 5-character CCD has been deposited. Details at wwPDB: PDB Entries w/Novel Ligands Now Distributed Only in PDBx/mmCIF & PDBML File Formats wwpdb.org/news/news?year…
Trying out one of these AI translation apps (@HeyGen_Official). I read the intro to Watson & Crick 1953 in English. Translations including lip movement. I speak neither French nor German. How does this sound to a native speaker?
At #ISMBECCB2023, my talented students present their exciting work: 22 petabase search for structure prediction, structural clustering of AFDB, IDP multimer prediction, structural compression & metagenomic classification. Find us at poster B-036, B-038, B-039, B-040, B-114.
Our Marv stickers arrived just in time for #ISMBECCB2023. Stickers are available at our posters. I am looking forward to reconnect with old friends, make new connections, and learn about the latest in bioinformatics. See you in Lyon.
What is the umpire doing??? She needs to get a new job ASAP, I agree with you @rennaestubbs 👍 I can't believe what I just saw!!!
erasing the ball mark and celebrating when your opponent retires from the match is a new low for sportsmanship in tennis
Our most recent piece of work "The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures" has just been released on bioRxiv (lnkd.in/esgbz-Gg)!!
I'm excited to share that I'll be joining @MITBiology as an Asst Prof. in Jan 2024! Come join us! 🤓🧪🖥️🧬
Thanks to these maps, we can now better understand things that were previously difficult to comprehend. 🌍
See our new perspective in JCIM on successful data sharing initiatives in chemistry and the implications for organic reaction data and the Open Reaction Database: pubs.acs.org/doi/10.1021/ac… (with @StevenKearnes and Rocío Mercado)
Introducing #ProfGPT, my new AI Avatar by @synthesiaIO! Getting closer towards fully automating myself :)
My group and I are excited to join this years #ISMBECCB2023 in Lyon. We are present 11 posters and 4 talks. We are preparing a set of updated stickers of our methods for the poster session. Sneak peek below!
@mpi_nat @SeoulNatlUni @JohannesSoeding @thesteinegger Foldseek gives AlphaFold protein database a rapid search tool, via @Nature nature.com/articles/d4158…
Foldseek, our fast structural aligner, is now published @NatureBiotech. It allows you to search through large structural databases like #AlphaFold or #ESMatlas in seconds. A long journey since '18! 1/6 📄nature.com/articles/s4158… 💾foldseek.com 🌐search.foldseek.com