Egor Marin's Avatar

Egor Marin

@marinegor.bsky.social

ML Scientist @ ENPICOM B.V. (Den Bosch, Netherlands) computational biology, ML, protein design, cheminformatics, fancy dev tooling, tinge of bouldering https://marinegor.dev

268 Followers  |  547 Following  |  86 Posts  |  Joined: 16.09.2023  |  2.0452

Latest posts by marinegor.bsky.social on Bluesky

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1. you get rate limited from @hf.co
2. you go to the page with rate limits, given you by 429 error
3. you get rate limited๐Ÿซ 

03.12.2025 23:15 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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rustedpy rustedpy has 3 repositories available. Follow their code on GitHub.

kinda reminds me of these projects: github.com/rustedpy

sadly neither `maybe` nor `result` are not maintained anymore๐Ÿ’”

27.11.2025 22:40 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

that was actually my motivation behind choosing a uni: I deliberately went for the one offering most flexibility throughout the bachelor, and ended up using it to its maximu.

23.11.2025 18:40 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

damn that's complicated! I guess i'm too lazy to go that deep๐Ÿ˜

ah, and caps is language switching for me, also insanely useful.

23.11.2025 10:49 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
4.2.4. Parallel analysis โ€” MDAnalysis 2.10.0 documentation

hey Pablo, congrats on the publication!

I imagine you started working on it before MDAnalysis introduced parallelization, so I wonder if you'd be interested in implementing it for eRMSF as described here: docs.mdanalysis.org/stable/docum...

22.11.2025 23:28 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

<<<< binding right cmd to escape

22.11.2025 23:02 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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So your data are available upon reasonable request? Well, we are making some reasonable requests - at scale. :)

1. Search literature (currently stubbed)
2. Enumerate papers, extract contacts
3. Send email w/ data drop location
4. Parse data

Does anyone want to help productionize this?

21.11.2025 21:32 โ€” ๐Ÿ‘ 5    ๐Ÿ” 1    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

please tell me there was "rust is blazingly fast" option

17.11.2025 20:45 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
In-person participants at the MDAnalysis 2025 User Group Meeting (online participants not shown).

In-person participants at the MDAnalysis 2025 User Group Meeting (online participants not shown).

The 2025 MDAnalysis User Group Meeting wrapped up. If you want to see what great talks and workshops we had, have a look at the UGM2025 repo github.com/MDAnalysis/U... . It was fantastic to have so many of you in Arizona and joining online! See you all again soon.

12.11.2025 00:09 โ€” ๐Ÿ‘ 12    ๐Ÿ” 3    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 3

I checked Plank and Einstein obituaries -- they've referred as Dr all throughout. But I guess it's, unfortunately, not the worst disgrace she's had throughout.

09.11.2025 16:49 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

within 24h, someone who I never comes in with a chunky PR that a) is more concise than my code, b) fixes all of my issues, c) also fixes relevant documentation for that. All I had left to do is to add this person to the changelog.

Feels unexpectedly good, I should say.

06.11.2025 12:29 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

Just had my "damn I love open-source" moment yesterday: have been struggling with a custom new reader for @mdanalysis.bsky.social, spent two big evenings on that, and decided to let it go and just ask for help in org's discord & github.

06.11.2025 12:29 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

I immediately wonder if there's any preference for antibody fold around heavy/light chain variable fragment length๐Ÿค”

27.10.2025 21:19 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

>Send me a message for any questions

it seems that your DMs are closed, could you double-check your privacy settings please?

10.10.2025 13:49 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

yep, it was Andre Geim, IgNobel for diamagnetic levitation (funny flying frog, it's also on youtube) and Nobel for graphene

03.10.2025 22:41 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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people at apple rn

25.09.2025 08:01 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

impressive maps!

aren't you worried that someone might guess your target based on these maps and e.g. scoop you?๐Ÿซฃ

22.09.2025 09:07 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

and afaik it's implementation-dependent, so for example pypy could've done things differently

21.09.2025 14:59 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

it honestly looks like the same shape in different colors, copypasted across the plot๐Ÿ˜

19.09.2025 10:34 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

that's a t-shirt idea right here

18.09.2025 13:27 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

oh that's a great one

there was also a weak negative correlation between model quality and a journal impact factor, I recall -- high(est) impact papers tend to focus on more challenging targets, which results in lower resolution and worse QC scores for the model.

14.09.2025 10:29 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

I think the first in line was some ide that forked PyCharm community edition, but I forgot the name :)

08.09.2025 20:13 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

on a more serious note, you might try referring to the existence of a strong Rust community in the country of application, and say that it'll help you to soften the bus factor and grow the community further๐Ÿคทโ€โ™‚๏ธ

03.09.2025 11:03 โ€” ๐Ÿ‘ 2    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

I honestly believe that the "career impact" section of a grant application should look like a single sentence saying "no grant -- no career"

03.09.2025 11:00 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

so you're saying that perhaps this self-censorship is limiting reviewers from writing good reviews?

21.08.2025 08:22 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

>diffusion-based antibody-specific NNs wouldn't do this?

why though? when it comes to antigens, they definitely memorise the interface, as per recent independent benchmark๐Ÿ˜

16.08.2025 05:54 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

oh sorry, by models I meant which NNs, not antibody structures

15.08.2025 14:57 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

do you have a list of antibody-specific models that you tested?

15.08.2025 13:35 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

oh, I actually recall one case, but for membrane homo-trimers GltTk and GltPh -- there are structures of both in the same space group. Can't find quickly, but I'm certain they exist :)

11.08.2025 10:06 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

I haven't seen that (worked with GPCRs and P450 enzymes), although technically there are no limitations.

But many times saw "one protein gets crystallised in many different space groups even within one crystallisation drop"

10.08.2025 15:13 โ€” ๐Ÿ‘ 1    ๐Ÿ” 0    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

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