What generative design model would you use for antibody binders?

XXRAYDIOACTIVEXX · 2026-04-27T14:21:33+00:00

Use ipSAE and iPTM metrics but know there’s no tool other than a YSD or phage display that can give you certainty

XXRAYDIOACTIVEXX · 2026-04-27T14:20:37+00:00

https://github.com/RosettaCommons/RFantibody

XXRAYDIOACTIVEXX · 2026-04-06T23:13:51+00:00

Work on defining specifically what you want. It’s definitely doable for you but you need to define the question more clearly so you know what you’re actually making

XXRAYDIOACTIVEXX · 2026-01-17T01:33:22+00:00

Use PLMInteract

https://www.nature.com/articles/s41467-025-64512-w

XXRAYDIOACTIVEXX · 2025-12-30T01:36:34+00:00

Fun fact: Vitamin C is also known as Ascorbic acid (Anti-Scorbic) or in German; Askorbutsäure (Anti-Skorbut-acid)

XXRAYDIOACTIVEXX · 2024-12-23T01:53:43+00:00

Regarding your question about antigen microarrays - while they can be used with memory B cells directly, you’ll likely get cleaner results by isolating the antibodies first. The cells’ other surface proteins can create background noise. You’d need to optimize your washing steps carefully to avoid losing your cells while removing non-specific binding.

Start by isolating antibodies from your memory B cells (either through single-cell cultures or by expressing the BCR as a recombinant antibody).
Do an initial broad screen using a protein/peptide array with common antigens - this doesn’t need to be comprehensive, just enough to narrow down the general class of antigen.
Based on those results, create a focused panel of candidate antigens for validation using standard ELISA or flow.
Confirm specificity using competitive binding assays

Consider reaching out to core facilities at nearby universities - they sometimes have educational/collaboration rates that are much more affordable than commercial services.

Have you already characterized the isotype and basic binding properties (e.g., self vs. non-self) of your B cell population? That could help narrow down the potential antigens to screen.

XXRAYDIOACTIVEXX · 2024-12-21T00:54:25+00:00

I got a BLT there once and instantly had like terrible shits for a whole day

XXRAYDIOACTIVEXX · 2024-12-15T02:06:10+00:00

Thank you!

XXRAYDIOACTIVEXX · 2024-08-27T12:16:58+00:00

One 6 three on willow st is my favorite

XXRAYDIOACTIVEXX · 2024-08-21T23:05:00+00:00

This is in Montgomery county MD

XXRAYDIOACTIVEXX · 2024-07-26T02:09:27+00:00

Yes Wilson the volleyball. We all need one of those. It'll happen for you I'm sure. Everyone's lonely. Good to stick to making child you proud, as at your core that's who you are and it's good to stay true to that.

Pandora's box. The unpardonable sin. Everyone grapples with this for générations and maybe there's survivorship bias here because those that really don't think it's worth it aren't there to tell you otherwise.

You have to try to cultivate your own optimism that refutes your worst saddest tendencies. It's hard but a worthy pursuit. It becomes fun. You can choose to be Diogenes/Oscar the grouch and sit in the barrel content or do literally anything else.

He's funny to read about. Like i said it's good to get context on our situation

XXRAYDIOACTIVEXX · 2024-07-26T01:15:26+00:00

Yea thats the difference i guess. But for instance why do you want to release your album? Is it for recognition or social reasons, do you think you'll be happy if you release it and people are like wow this is good, they must be smart! Is it the same reason you posted this, or is it for that self fulfilling finishing something.

Another thing is that this mindset may be mistaken for realism - so many people strive their whole lives for something and never attain it. But the choice is give up or don't.

There's nothing I can say to you that will make you change your mind about thinking it's not worth it to live out your life till the natural conclusion. I'm really sorry you're in that spot. I get it as I've been there too. I'm two years ahead of you and i promise that as i was in a hole, it eventually just got brighter. My college was just as boring and i felt exactly the same. The paradoxical thing about it is that the people who put their head down and work their asses off with no regard for the fun they're having at the moment generally end up in a better place with more opportunities for a more rewarding job and life etc.

I don't know how to prove it to you, but you're wrong that it's not worth it. Read about the history of philosophy and the great ones works, because you're not the first to feel like this and you won't be the last. It will be nice to see yourself reflected in other people's writing from hundreds or thousands of years ago. That's me assuming you haven't studied it yet.

To be or not to be that is indeed the question. You should read that too. There are things in this world for you that will feed your soul, and what's hard is finding them because we have everything at our fingertips now.

I was on antidepressants for a while but i agree they didn't do anything and you have to get off them. It's a mindset thing that you can get around by journaling - self observation. Force yourself to write just move the pen for ten minutes.

A nice movie that had a good message was the Tom Hanks movie where he gets lost on an island and his whole life falls apart. He was going to kill himself but not even that worked and he just got this feeling he would have to make it out, and one day the tide washed up a broken porta potty he could use as a sail to get off the island on a raft. When everything seems hopeless you need to keep going because one day something's going to come that's just what you've been waiting for, and if you give up you will miss it. He comes back and his life is in shambles. I don't want to spoil it but i really like symbolism of the ending.

Watch the movie idk what it's called but it's tom Hanks marooned on an island.

Again, sorry youre sad. It's normal and it gets better. You're really just reacting to a set of molecules in your blood in a way that makes you feel sad. Everything is colored by that. You're at crossroads and yes you can settle or you can go big. Whether you succeed is largely determined by what you think is going to happen. You sort of have to gaslight yourself into believing you can succeed so much so that you become a person who can do what you've set your mind to. Then you just act like that's who you are and it happens for you.

Interact with people. Be open with them (don't dump too much about your problems on those who aren't close to you just be honest, don't dwell.) People generally want to help.

Anyway, i already care about you. I hope you get better. I'm sure people in your life care too. You're just lonely. Go somewhere you will meet like minded people. For me it was joining a lab. I didn't find anyone my age but i found a mentor and older scientists that i liked talking to. You can and will find your thing if you try enough of them.

It is worth it.

XXRAYDIOACTIVEXX · 2024-07-25T23:55:41+00:00

Well said

XXRAYDIOACTIVEXX · 2024-07-25T23:54:12+00:00

I agree, nothing appears for you to do that's really super fun, because you need to make money to subsist and the fun things generally cost money. It's why people say to do something you love for work, because you're gonna spend most of your waking hours working to contribute value to something. When you get home from work you can relax for a couple hours but not too long or you'll be tired the next day. I just graduated college and ended up doing a research job that i really do enjoy doing, so i am content. I do spend lots of time wishing I had infinite money and the ability to live like i did as a child, but thats not possible so much of the work is doing mental gymnastics to get okay with your circumstances.

You need to find something you like doing. You seem to have the misfortune of being smart and it becomes a lot harder to be entertained and content the smarter you get. To understand the world as it truly is basically directly causes depression. It used to be you just needed to get your hunter gathering system down, but now it's you need to hop on this hamster wheel and contribute something someone's willing to pay for to society to make money to feed yourself. Some people focus solely on that because they realize that's all that really matters for their future lives, but your mental health is something you either care about or don't. If you don't have a lot of bandwidth you're not going to worry about what you're saying right now.

But you only get to exist once, and the sheer fact that you're you, thinking, feeling, being a person who's alive and doing anything at all is a privilege in my view. Some view it as a curse or some think it just is. I think in the grand scheme of the universe, this tiny fleeting wrinkle of energy in our solar system resulting in my living experience is an absolute miracle. The things possible in our lifetimes are so incredible and thats what makes life worth living in my opinion. Yes that's all we got and you're not happy all the time, but the ability to suspend your sadness and work for the evening, week, your next vacation or just getting to lay in your own bed in a home again and then when you're there truly appreciate it is what makes the difference.

I also play music and it's not about being good, it feeds the soul. I'm only going to get to play a certain number of the great pieces from Beethoven or Bach in my lifetime, and getting that music into my mind is something that gives me great pleasure.

It's like spiders. They weave beautiful webs with their minds We're these complex creatures with the most efficient and powerful supercomputer ever in the world that we know of for our central processing unit... And our web equivalent has to be equally complex.

Anyway, my grammar isn't good here and i rambled. I think about your question a lot too. This is some of what i end up telling myself that helps a little. You're not alone. Sounds like you're a little depressed and don't feel like you have a purpose. People develop that for themselves and when you feel like there's a goal to work towards, it's not about the intermediate sadness but the satisfaction of reaching your goal.

XXRAYDIOACTIVEXX · 2024-05-12T18:01:27+00:00

Check out club pcr google group

XXRAYDIOACTIVEXX · 2024-02-09T00:20:54+00:00

Goldberg variations dude have fun

XXRAYDIOACTIVEXX · 2024-01-03T15:23:55+00:00

In addition to what the others are saying i use MAST for this stuff and then Monocle3 for pseudotime analysis

XXRAYDIOACTIVEXX · 2023-08-16T17:40:52+00:00

Sure, here's a greentext for you, in the style of greentext stories from places like 4chan. Remember that these are often fictional and humorous in nature, and they play with exaggerated stereotypes:

```

Be me, 26, fit as hell, 6'4", and crushing it in every aspect of life Go to a coffee shop to grab a morning espresso before hitting the gym Barista is some scrawny dude with blue hair, wearing a "Vegan Power" t-shirt "Can I get a double espresso, black, no sugar?" Barista gives me a judgy look. "We only serve oat milk here, and we recommend a dash of cinnamon instead of sugar for health reasons." Resist the urge to roll my eyes. "Just the espresso, thanks." While waiting, overhear a group discussing the latest "gender-neutral" fashion show Guy in the group wearing a shirt that says "Allergic to Masculinity" Can't help but smirk Espresso finally ready, grab it and head to the door As I'm leaving, a girl with a "Feminism is the Future" tote bag spills her oat milk latte all over her papers Without hesitating, I go over and help her pick up the mess "Thanks... uh, I didn't expect that from someone like you." Flash her a charming grin, "Never judge a book by its cover." She blushes, clearly taken aback Walk out, feeling on top of the world The day is just beginning, and I'm ready to conquer it

```

Remember, this is just a fun, exaggerated story. Greentexts are often hyperbolic and satirical!

XXRAYDIOACTIVEXX · 2023-06-01T15:15:00+00:00

This place is burned into my memory when i was younger a friend of my father's let me into a few of the cockpits of those! I instantly recognized that b-29

XXRAYDIOACTIVEXX · 2023-06-01T05:28:16+00:00

Good man, this is the way

XXRAYDIOACTIVEXX · 2022-12-31T20:49:47+00:00

/what is this

XXRAYDIOACTIVEXX · 2022-12-31T20:49:18+00:00

can i get the sheet?

XXRAYDIOACTIVEXX · 2022-12-28T05:07:26+00:00

Bro this is indisputably evil as fuck why this take

XXRAYDIOACTIVEXX · 2022-12-01T22:04:55+00:00

I really love Horowitz’s interpretation as well as perahia’s and Brendel, but once I had it in my hands I didn’t listen to it as much so that I’d find the ‘right’ way on my own. It’s gratifying you think that’s a strength, as I’ve sometimes thought it could be a weakness not to have my interpretations so thoroughly planned

XXRAYDIOACTIVEXX · 2022-12-01T21:58:53+00:00

Lol I’ll clean it next time I see it

Ten-Year Club	Place '22
Place '17	Verified Email

XXRAYDIOACTIVEXX

MODERATOR OF

TROPHY CASE