Rosetta Commons

Members of the IPD: Gaurav Bhardwaj, Frank DiMaio, and 2024 Nobel laureate David Baker have unveiled a deep-learning framework capable of the de novo design of macrocyclic peptides that bind proteins with nanomolar affinity and remarkable precision. This work is based on a report from June 20, 2025, in Nature Chemical Biology Read more here: https://lnkd.in/g5WEyfGN

Looking for jobs in the field of synthetic biology? We have added 8 new open positions to our SynBio Job Board for early, mid-career and late-career professionals. These positions are open to undergrads, masters level students, Ph.D.s, postdocs or individuals planning on working in the synthetic biology industry, academia or governance. Discover synbio career opportunities on our job board! https://lnkd.in/ddHa-jrS #Jobs #synbio #synbiojobs

𝗘𝗠𝗕𝗢 𝗣𝗿𝗮𝗰𝘁𝗶𝗰𝗮𝗹 𝗖𝗼𝘂𝗿𝘀𝗲 | 𝗔𝗜 𝗳𝗼𝗿 𝗽𝗿𝗼𝘁𝗲𝗶𝗻 𝗱𝗲𝘀𝗶𝗴𝗻 (𝗔𝗜𝟰𝗣𝗗) 𝟮𝟬𝟮𝟱 🚨 𝗙𝗶𝗻𝗮𝗹 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿: 𝗥𝗲𝗴𝗶𝘀𝘁𝗿𝗮𝘁𝗶𝗼𝗻 & 𝗔𝗯𝘀𝘁𝗿𝗮𝗰𝘁𝘀 𝗖𝗹𝗼𝘀𝗲 𝟭 𝗔𝘂𝗴𝘂𝘀𝘁 𝟮𝟬𝟮𝟱! We’re just days away from the deadline to apply for a spot to attend the EMBO Practical Course on AI for Protein Design (AI4PD) in Puerto Varas, Chile, taking place between Nov 3–9, 2025. 🎯 𝗪𝗵𝘆 𝗬𝗼𝘂 𝗦𝗵𝗼𝘂𝗹𝗱 𝗔𝘁𝘁𝗲𝗻𝗱: - Zero registration fee for the selected students/postdocs! Industry participants pay a registration fee €1,000 and academics pay a registration fee of €500 - EMBO has travel grants, child care grants and accessibility awards available! - Shared hotel accommodation + breakfast, lunch, dinner & coffee breaks for the duration of the conference (arrivals on Nov 2 and departures on Nov 9). - Hands-on tutorials with AI tools like AlphaFold2, RoseTTAFold, RFDiffusion, ProteinMPNN, Frame2seq, and more! - Design your own proteins using AI tools in real time during the Hackathon! - Share and learn alongside an international cohort with diverse expertise and perspectives - Hike with us on Saturday, and receive exclusive event swag. ✅ 𝗔𝗰𝘁𝗶𝗼𝗻 𝗦𝘁𝗲𝗽𝘀: - Submit your application and abstract by 𝗔𝘂𝗴𝘂𝘀𝘁 𝟭, 𝟮𝟬𝟮𝟱 - Await acceptance decision by 𝗔𝘂𝗴𝘂𝘀𝘁 𝟭𝟰, 𝟮𝟬𝟮𝟱 - Complete payment by 𝗔𝘂𝗴𝘂𝘀𝘁 𝟮𝟮, 𝟮𝟬𝟮𝟱 - Plan your travel to Puerto Varas, Chile in early November — accommodation & meals are on us! This exciting course is sponsored by EMBO, Rosetta Commons, The Protein Society, AI Proteins, Kura Biotech, Patagonia Biotech HUB, Google Colab and led by chris bahl, Alena Khmelinskaia, Nicole Lehna and myself. Don’t miss this chance to build AI-driven protein design expertise, collaborate with international peers, and push your research to the next level—all while immersed in the natural beauty of southern Chile. Apply now and join the future of protein engineering! #EMBOaiProteinDesign https://lnkd.in/evb-2gf2

“Docendo Discimus”: By teaching we learn. As most people here know, I LOVE to teach. That’s why it brings me such great joy to say that I recently finished co-teaching BioCÅmp w Fatima Davila (and help from Alisha S., Camille Mathis), a 2 week intensive summer program where we gather HS students from around Baltimore and teach them various computational modeling techniques. As my second year teaching this program under Jeffrey Gray, it brings me so much joy to see approximately 15 recruited students learn about the computational techniques I use daily for my research. From drawing amino acids by hand on the board to figuring out how to use Monte Carlo algorithms to predict the stock market, the students were challenged everyday in a healthy, conduicive environment. This year, with a revamped course, the students learned about basic chemistry, biophysics, thermodynamics, programming logic, MC algorithms, protein evolution/engineering, and Machine Learning (especially linear regression by hand, which they all “loved”) in the span of 2 weeks. Of course, anyone can regurgitate information, so the best way to learn is with a hands on project where students can apply the knowledge and solidify their new skills! So their final project this year involved taking an experimental crystal structure, explaining it, then folding its sequence using an energy minimization MC simulation and comparing it to current AI methods (AlphaFold3, Chai1 and Boltz2). The students had an amazing time learning and I had an amazing time teaching! I would like to thank Rosetta Commons, the Open Molecular Software Foundation, and The Johns Hopkins University DSAI center for sponsoring our program and allowing these students the ability to pursue their intellectual passion in a time of extreme funding uncertainty. Excited to see them grow and I hope to have the opportunity to teach this program again. #engineering #chemicalengineering #experience #research #leader #learning #biotechnology #thankful #blessed #blackinstem #blackexcellence #inspire

I am very excited to join Parisa Hosseinzadeh's lab group at RosettaCon next week! I will be presenting my work for our project titled "Computational Design of Cyclic Peptide Mu-Opioid Receptor Agonists via De Novo and ML Anchor Extension" (Poster 15 at 8:30 PM on Monday, August 4th). I can't wait to see everyone from the 2025 Rosetta Commons REU cohort and meet lots of new people!

Registration for the Biomolecular Modeling and Design with Rosetta and ML Tools Workshop (November 17–19, 2025) is now open. The goal of the workshop is to educate and train academic and industry users on the Rosetta software suite. Explore more: meilerlab.org/tutorials/

We're excited to introduce our #RaMP 2025-2026 cohort. Watch this space for more updates.

🌟 Exciting News!🌟 After thoughtful reflection and a period of exploring my options, I’m thrilled to share that I’ve accepted an offer to join the National Science Foundation (NSF) -funded Rosetta Commons REU program this summer! I’ll be conducting research at Rutgers University–New Brunswick in the Sagar Khare Laboratory in New Jersey. In the Khare Lab, I’ll be learning how to design a protein that can bind to Erythrosine (a recently banned carcinogenic dye) using computational protein design and experimental characterization. Additionally, I will be completing Python coding school at Johns Hopkins in the first week of my research path. The lab’s mission is to develop a predictive understanding of enzymatic structures in areas like: 1. Biodegradation of environmental pollutants 2. Advancing cancer treatment 3. Designing catalytic protein drugs This opportunity represents not just a learning experience, but a meaningful step toward my long-term goal of contributing to impactful and meaningful scientific research in the molecular biology field. Thank you to everyone who has supported my journey so far — John Weldon (Research Lab mentor), Matthew Hemm (Molecular Biology professor), and Daniel Anoruo (a close friend) for helping me find this opportunity and giving me tips on my application. And most importantly, thank you to my parents for supporting me throughout this process. Truly, I am grateful. I cannot wait to share what I learn over the summer! #NSFREU #JohnsHopkins #KhareLab #ProteinDesign #MolecularBiology #ComputationalBiology #UndergraduateResearch #STEM

Do you want to use #bindcraft to use #ai to design mini protein binders for research? Are you worried about IP considerations but also want to get great results? http://Levitate.bio, part of Rosetta Commons is the only commercial provider of API and easy-to-use graphical interface #bindcraft with all Rosetta options available under a clean set of licenses with University of Washington. (Expert CLI users can run on their prem or cloud with Rosetta and open source licenses, of course, and may not need help from Levitate) The protein #ai field is moving forward rapidly but in many cases we need Rosetta Commons e.g. for optimal scoring with bindcraft with "more discriminatory power" according to Pacesa et al I am excited to see how Levitate Bio LLC and Rosetta Commons can work together to bring the best protein design tools to a broader audience, without compromises on output quality or model filtering. At Cyrus Biotechnology we use a range of novel AI tools, especially our own MHC II peptide datasets and proprietary AI model HIDES for biologics immunogenicity, and #bindcraft is emerging as a key #ai research tool to quickly generate tight binding mini proteins as an alternative to research-grade mAbs. This is especially useful for academic labs looking for some labels for use in cell-based assays, or for companies working on new target validation, among other applications. In other words, if you want the best in reliable & easy-to-use mini binder protein design, levitate.bio is the Champagne option. Everything else is just sparkling protein design.

Greetings from the Beaver State! It has only been a little over a month since I began my REU fellowship with Rosetta Commons and the Phil and Penny Knight Campus for Accelerating Scientific Impact at the University of Oregon, but it's safe to say it has been a magical experience so far! I am looking forward to sharing more about the exciting work I have been doing with the Protein Builders in Parisa Hosseinzadeh's lab, but in the meantime, enjoy this picture from Salt Creek Falls. Fun Fact: This waterfall is notable for its main drop of 286 feet, ranking third highest among plunge waterfalls in Oregon!