16 Replies to “David Baker (U. Washington / HHMI) Part 1: Introduction to Protein Design”

  1. awesome, let's suppose sometime in the future we reach the level that we are capable of creating all essential elements in 3d all way down to electrons, program all laws of physics of the universe on a molecular level, start a virtual universe by launching the big bang in virtual reality and watch it as it evolves when all these elements randomly combine and interact with each other?
    will it evolve to produce intelligent 3D human beings capable of thinking and doing the same in their virtual reality? and..
    are we the product of such achievement?

  2. Hi,
    Im currently working on a presentation for my studies about that exact theme. My Information’s are based on an article from the Nature magazine from the 15th September of 2016. In the article the scientists also use the Rosetta program to design proteins. In my understanding they first try to build the carbon backbone structure by finding the lowest energy state, and then they try to add the different sidechains for the tightest packing together with the lowest energy possible. Here is my question: Don’t alpha helices and ß sheets need specific amino acid residues to even exist, at least at some places? If so does the program calculate these specific amino acids into the primary structure to stabilize the secondary structure?

    Ps: The name of the article is: The Protein World

  3. Fascinating. Designing, optimizing, implementing and integrating custom proteins. I had no idea this was possible.

    It's worth noting, however, that the discovery of the magnitude of intelligently-directed computer resources needed to make one protein is a strike against the possibility that undirected natural processes could have come up with any protein.

  4. And I thought that the conformation that a protein adopts isn’t necessarily the global energy minimum, but rather a local energy minimum, where the protein would have to overcome a barrier to adopt the global energy minimum

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