cryo2go

cryo2go

cryoEM related publications discussed with the authors, to get the story behind the science. If you have comments, questions, complaints or requests for a specific paper, please hmu on Twitter @cryo2go with a link to the episode.

Episodes

November 27, 2021 77 mins
In this episode, Ellen sits down with me to talk all things cryoDrgn ❄️🐉

Full transcript available at (https://github.com/bHimes/cryo2go/tree/main/transcripts/2020_EllenZhong_cryoDrgn)

cryoDrgn is the software she developed during her PhD to model continuous heterogeneity in cryoEM data. She uses a combination of coordinate MLP and variational autoencoders to do so. Listen in if you'd like to know more about what that means! We als...
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In this episode, we get to hear from Dr. Christopher Barnes, currently at Caltech, about his research combining structural biology and immunology. Christopher was able to rapidly deploy his expertise developed in studying the HIV virus to the emerging SARS-COV-2 outbreak early in the pandemic, publishing this article in May 2020.

See here in Cell (https://www.cell.com/cell/fulltext/S0092-8674(20)30757-1?_returnURL=https%3A%2F%2Flin...
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In this episode, recorded a few days after the bioarxiv paper was released in March 2020, Dari expands on his work developing a set of biological priors using machine learning, which can then be used to regularize cryoEM reconstruction/refinement.

We go beyond just the math and the methods and discuss the real what and why with respect to the motivation and prospects of this work.

"Exploiting prior knowledge about biological macromol...
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March 26, 2020 45 mins
We hear from Dr Kanika Khanna about optimizing cryo-FIB-ET and how she used the technique to advance our understanding of bacterial sporulation, as discussed in eLife:

https://doi.org/10.7554/eLife.45257.001

She also shared here outreach work with [Asha foundation | (https://sd.ashanet.org/)]

Her website can be found here (https://khannakanika11.wixsite.com/mysite/)
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March 1, 2020 34 mins
Phase contrast provides the best means to high resolution electron microscopy images. The phase shifts induced by the light atoms that make up biological specimens produce very little contrast, which is why we usually image out of focus. This takes advantage of phase shifts introduced by the CTF at the expense of more complicated image processing, and loss of information near CTF zeros.

Phase plates offer a potential solution, but h...
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February 7, 2020 29 mins
The first full episode. Mike Roberston tells about GEMSPOT, a pipeline for modelling ligands into their binding pockets that integrates constraints from the cryoEM map with traditional computational chemistry methods. The pre-print can be found on bioarxiv at doi: http://dx.doi.org/10.1101/750778

Mike is on twitter @BiophysicsGuy
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January 31, 2020 51 secs
I recorded my first interview a couple of days ago and have another scheduled for Saturday. I'm excited to get this thing rolling, so here's the intro, fresh off the mixer
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