flobosg

45 ms·

631.
by flobosg 4y ago
> If you're setting the ability to crystallize as the single point of failure endpoint, that logic applies to every subfield. I agree that there are other fields with similar issues. What baffles me is how long protein crystallizati
632.
by flobosg 4y ago
Homology search is a method to find homologous sequences, that is, evolutionary related sequences that posess a common ancestor. This was usually done based on how identical sequences were, but newer algorithms allow to find remote homologs
633.
by flobosg 4y ago
Because homology search is not homology modelling. And a multiple sequence alignment is not a structural (i.e, with three-dimensional coordinates) template.
634.
by flobosg 4y ago
> Nor can I support the assertion that structural biology students are subject to special abuse that regular grad students are not. I didn’t say anything regarding that. > This is true of pretty much any graduate work in molecular bio
635.
by flobosg 4y ago
Protein crystallization can be very difficult and there is no general solution. Kits that screen for crystal growth conditions usually help but optimization is needed in most cases. Then, that crystal must have certain properties that allow
636.
by flobosg 4y ago
* https://pdb101.rcsb.org/motm/ * https://ccsb.scripps.edu/goodsell/ * https://pdb101.rcsb.org/sci-art/geis-archive/irving-geis * https://www.digizyme.com&#x2
637.
by flobosg 4y ago
Rosetta methods are also moving towards ML. Here’s an article from last week: https://www.science.org/doi/10.1126/science.abn2100
638.
by flobosg 4y ago
Hear, hear. This is probably the best take.
639.
by flobosg 4y ago
> It ultimately relies on mapping sequence to structure. So does every structural prediction method. > if you give it a brand new fold with no relation to other folds, it cannot predict it That will depend on the number of effective s
640.
by flobosg 4y ago
> Yes, it has a very nice model of what sequences should look like in 3D. A structural model, you would say. > That model is derived from experimental data. That doesn’t make it a template-based model, or a homology one. > if I giv
641.
by flobosg 4y ago
This is a gross misrepresentation of the method.
642.
by flobosg 4y ago
Those databases are used to derive the evolutionary couplings and distance matrices used by the algorithm. Several of those databases aren’t even structural ones. Furthermore, AlphaFold can function with only a MSA as an input, without retr
643.
by flobosg 4y ago
> AlphaFold is amazing homology modeling If it is homology modelling, then how can it work without input template structures?
644.
by flobosg 4y ago
> And why we cannot just simulate protein behaviour and interactions using quantum mechanics? QM calculations have been done in proteins, but they’re computationally very expensive. IIRC, there are hybrid approaches where only a small po
645.
by flobosg 4y ago
Folding@home answers a related but different question. While AlphaFold returns the picture of a folded protein in its most energetically stable conformation, Folding@home returns a video of the protein undergoing folding, traversing its ene
646.
by flobosg 4y ago
This might be an interesting resource for you: https://pdb101.rcsb.org/
647.
by flobosg 4y ago
> very difficult crystal structure experiments? Apart from X-ray crystallography there are other methods for structure determination such as nuclear magnetic resonance (NMR) or cryo-electron microscopy (cryo-EM). The latter has seen a dr
648.
by flobosg 4y ago
Snap, or jounce, is the fourth derivative of position.
649.
by flobosg 4y ago
(2017) If you liked it, check out the work of Christian Bök, in particular “Eunoia”.
650.
I'm running a D&D campaign for my daughter and a friend over Zoom(twitter.com)
8 points by flobosg 4y ago|2 comments
651.
by flobosg 4y ago
Another use case for Bloom filters: Bioinformatics (see https://en.wikipedia.org/wiki/Bloom_filters_in_bioinformatic... )
652.
Being a Better Photographer(johnwdefeo.com)
4 points by flobosg 4y ago|0 comments
653.
Retraction with Honor(sociobiology.wordpress.com)
6 points by flobosg 4y ago|0 comments
654.
by flobosg 4y ago
Somewhat related: Fernando Pessoa: Office Worker, Occultist, Galaxy of Writers - https://news.ycombinator.com/item?id=28191843 - August 2021 (16 comments) The Politics of Fernando Pessoa - https://news.ycombi
655.
by flobosg 4y ago
I didn't say it was an entry point to modern anime.
656.
by flobosg 4y ago
Besides, Cowboy Bebop is a great entry point for someone who wants to get into anime.
657.
by flobosg 4y ago
Here’s another one: # For fuzzy-jumping down your home directory. # See http://richardmavis.info/fuzzy-jumping function fcd { cache=~/.config/home-dirs-list if (( $# == 0 )); then
658.
by flobosg 4y ago
I use an old Thinkpad x220 on a virtual console running micro.
659.
by flobosg 4y ago
(2017)
660.
by flobosg 4y ago
https://searchhut.org/about/domains returns 404, by the way.

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