Save the date! March 30 at 9:30-11:15 am PST is the IUBMB Trainee Initiative’s first event! And it’s one I’m SOOOOOOO excited for! We’re going to be learning all about protein structure prediction & design and how we can get started with the protein folding game Foldit! With talks, demos, & Q & A’s from/with Drs. David Baker and Brian Koepnick from the University of Washington, Seattle’s Institute for Protein Design. You can register (free) now! at https://tinyurl.com/register-proteindesign 

Here’s what’s on tap (text from last Friday’s post):

“The Coming of Age of De Novo Protein Design” Dr. David Baker wows us for 30 minutes then lets us ask him questions

“Applying Foldit to help stop COVID-19” with demo Dr. Brian Koepnick gives us a 40 minute webinar on Foldit – what it is, its application in the fight against COVID-19, and how we can get going with it

Q & A

All are welcome, trainees are extra welcome. 

Want to know even more??

Here’s Dr. Baker’s talk abstract: “Proteins mediate the critical processes of life and beautifully solve the challenges faced during the evolution of modern organisms. Our goal is to design a new generation of proteins that address current-day problems not faced during evolution. In contrast to traditional protein engineering efforts, which have focused on modifying naturally occurring proteins, we design new proteins from scratch based on Anfinsen’s principle that proteins fold to their global free energy minimum. We compute amino acid sequences predicted to fold into proteins with new structures and functions, produce synthetic genes encoding these sequences, and characterize them experimentally. In this talk, I will describe the de novo design of SARS-CoV-2 candidate therapeutics, synthetic antagonists and agonists of cellular receptors, molecular machines, and recent advances in deep learning-based structure modeling and design.”

More about the Baker lab: https://www.bakerlab.org/ 

Learn more about Foldit at their homepage: https://fold.it/portal/ & YouTube channel (with lots of talks from Brian too!): https://www.youtube.com/channel/UCGjfDFjL-7rvhRRl2keqhcA 

More about our speaker Brian Koepnick and his research here: https://briankoepnick.com/research/

More about how the Institute for Protein Design has helped combat COVID-19: https://www.ipd.uw.edu/coronavirus/

A great FEBS article about the online international Foldit community: https://network.febs.org/posts/learning-and-playing-foldit-in-an-online-community        

Some scientific articles featuring FoldIt:

Some of the Baker lab’s articles about deep learning and protein structure predictions & modeling:

  • Accurate prediction of protein structures and interactions using a three-track neural network. Baek M et al., Science. 2021 Aug 20;373(6557):871-876. doi: 10.1126/science.abj8754. Epub 2021 Jul 15. PMID: 34282049; PMCID: PMC7612213 DOI: 10.1126/science.abj8754 
  • Computed structures of core eukaryotic protein complexes. Humphreys et al., Science. 2021 Dec 10;374(6573):eabm4805. doi: 10.1126/science.abm4805. Epub 2021 Dec 10. PMID: 34762488; PMCID: PMC7612107. DOI: 10.1126/science.abm4805 

A cool perspectives piece on the combined roles of RoseTTAFold and AlphaFold: 

As for the IUBMB Trainee Initiative…

Our Mission: “The aim of the IUBMB Trainee initiative is to provide opportunities for emerging researchers of all levels. That entails access to our network and opportunities for skills development, training resources and a supportive team to help them in their professional and scientific journeys! Accessibility, diversity, and inclusion are most important to us. Whether you have limited access to resources, are a first-generation scientist trying to navigate the world of academia, or face visible and invisible barriers-we want to make the “invisible curriculum” open to everyone who wants to explore the world of Biochemistry and Molecular Biology. So, whether you are trying to build a career in academia or outside of it, advance your learning or just explore, we hope to have something for you!”

Learn more here: https://iubmb.org/iubmb-trainee-initiative/ & https://bit.ly/iubmbtrainees 

Join our “Friends of the IUBMB” Mailing list here: https://t.co/9LwF6Sd6aV 

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