#protein-structure-prediction

[ailifehacks]

How AI in Protein Folding Is Revolutionizing Structural Biology and Drug Discovery

Explore how AI in Protein Folding is transforming structural biology, drug discovery, and protein structure prediction across the USA and globally. What Is Protein Folding and Why AI Matters in Structural Biology Proteins perform critical functions in the human body, but their functions depend entirely on their unique 3D structure. Predicting how a linear amino acid chain folds into complex 3D…

[smol-blue-bird]

not to sound like an obnoxious ChatGPT shill, but the way some people talk about AI on this website is absolutely ridiculous. AI technology helping researchers discover how proteins fold is not the same as freshmen using chatbots to cheat on their homework. C'mon, guys

[chocosvt]

:]

[mehmetyildizmelbourne-blog]

Why I Believe AlphaFold 3 is a Powerful Tool for the Future of Healthcare

Insights on a groundbreaking artificial intelligence tool for health sciences research Dear science and technology readers, Thanks for subscribing to Health Science Research By Dr Mike Broadly, where I curate important public health content. A few months ago, I wrote about AlphaFold 3, a groundbreaking AI tool that helps scientists understand protein structures, which are essential for…

[reasonsforhope]

"A team at Northwestern University has come up with the term “dancing molecules” to describe an invention of synthetic nanofibers which they say have the potential to quicken the regeneration of cartilage damage beyond what our body is capable of.

The moniker was coined back in November 2021, when the same team introduced an injection of these molecules to repair tissues and reverse paralysis after severe spinal cord injuries in mice.

Now they’ve applied the same therapeutic strategy to damaged human cartilage cells. In a new study, published in the Journal of the American Chemical Society, the treatment activated the gene expression necessary to regenerate cartilage within just four hours.

And, after only three days, the human cells produced protein components needed for cartilage regeneration, something humans can’t do in adulthood.

The conceptual mechanisms of the dancing molecules work through cellular receptors located on the exterior of the cell membrane. These receptors are the gateways for thousands of compounds that run a myriad of processes in biology, but they exist in dense crowds constantly moving about on the cell membrane.

The dancing molecules quickly form synthetic nanofibers that move according to their chemical structure. They mimic the extracellular matrix of the surrounding tissue, and by ‘dancing’ these fibers can keep up with the movement of the cell receptors. By adding biological signaling receptors, the whole assemblage can functionally move and communicate with cells like natural biology.

“Cellular receptors constantly move around,” said Northwestern Professor of Materials Sciences Samuel Stupp, who led the study. “By making our molecules move, ‘dance’ or even leap temporarily out of these structures, known as supramolecular polymers, they are able to connect more effectively with receptors.”

The target of their work is the nearly 530 million people around the globe living with osteoarthritis, a degenerative disease in which tissues in joints break down over time, resulting in one of the most common forms of morbidity and disability.

“Current treatments aim to slow disease progression or postpone inevitable joint replacement,” Stupp said. “There are no regenerative options because humans do not have an inherent capacity to regenerate cartilage in adulthood.”

In the new study, Stupp and his team looked to the receptors for a specific protein critical for cartilage formation and maintenance. To target this receptor, the team developed a new circular peptide that mimics the bioactive signal of the protein, which is called transforming growth factor beta-1 (TGFb-1).

Northwestern U. Press then reported that the researchers incorporated this peptide into two different molecules that interact to form supramolecular polymers in water, each with the same ability to mimic TGFb-1...

“With the success of the study in human cartilage cells, we predict that cartilage regeneration will be greatly enhanced when used in highly translational pre-clinical models,” Stupp said. “It should develop into a novel bioactive material for regeneration of cartilage tissue in joints.”

“We are beginning to see the tremendous breadth of conditions that this fundamental discovery on ‘dancing molecules’ could apply to,” Stupp said. “Controlling supramolecular motion through chemical design appears to be a powerful tool to increase efficacy for a range of regenerative therapies.”"

-via Good News Network, August 5, 2024

[hellsite-proteins]

Let's try the legendary Brain Power chorus:

Let the bass kick

O-0000O00000 AAAAE-A-A-|-A-U- JO-

O0000O00000O AAE-O-A-A-U-U-A- E-eee-ee-eee AAAAE-A-E-I-E-A- JO-000-00-00-oo EEEEO-A- AAA-AAAA

O-o000o00000 AAAAE-A-A-l-A-U-JO-

O00000000000 AAE-O-A-A-U-U-A- E-eee-ee-eee AAAAE-A-E-|-E-A-

JO-o00-00-00-0o EEEEO-A-AAA-AAAA

O-o00O00000o AAAAE-A-A-|-A-U- JO-

O0000O00000o AAE-O-A-A-U-U-A- E-eee-ee-eee AAAAE-A-E-I-E-A-

JO-000-00-00-0o EEEEO-A-AAA-AAAA-

O---------

oh i am very interested to see how this turns out

letter sequence in this ask matching protein-coding amino acids:

LettheasskickAAAAEAAAAAEAAAEeeeeeeeeAAAAEAEIEAEEEEAAAAAAAAAAAAEAAlAAAEAAAEeeeeeeeeAAAAEAEEAEEEEAAAAAAAAAAAAEAAAAAEAAAEeeeeeeeeAAAAEAEIEAEEEEAAAAAAAA

protein guy analysis:

well this is a long one. and by that i mean that the structure itself is just one long helix. for what it's worth, the confidence is pretty good. this makes enough sense, given that both alanine (A) and glutamate (E) tend to prefer to be in alpha helices. overall, this is just a silly little guy and i'm very happy with it

predicted protein structure:

[cryptotheism]

"The mutational experiments of the A and B domains of protein G raise many questions. Can we ever hoe to simulate folding of a protein, or even to predict its structure, if a single amino acid difference determines which of two folds a protein adopts? This is the "Paracelsus Curse" to computational and theoretical biochemists. The [Paracelsus] challenge is now much greater. At present, the effect of such minimal mutations on conformation cannot be predicted."

--Proteins: Concepts in Biochemistry (Almeida, 2025)

COOL

[moncherriecoups]

Muted Hearts - Before Us

The one who let me know and see myself

You are my only reason

If you'll remember me forever

Then it's okay for me to get hurt

My heart carved with your light

Only makes me stronger

Your sharp thorns, please give it to me

'Cause you're my flower

Chapter 10.2

February 2024

Seungcheol didn’t particularly like change.

His life was structured—schedule after schedule, practice, meetings, rehearsals, workouts. If he could keep at least one thing constant, he would. And for the longest time, that one thing was the gym in the company building. It was close, private, and most importantly, familiar.

But then came Kim Mingyu.

"Hyung, please," Mingyu had whined, practically draping himself over Seungcheol's back after practice. "I found this gym, and it’s so much better than the one at the company. The vibe is cozy, the equipment is brand new, and they even have protein shakes made fresh at the counter—fresh, hyung!"

Seungcheol had barely looked up from his phone, already suspicious. "Then go by yourself?"

"I hate going alone."

Of course he did. Mingyu was practically a golden retriever in human form—thrived in companionship, hated doing anything solo. But Seungcheol wasn’t about to be dragged across town just because the younger one wanted a change of scenery.

Until Mingyu pulled out the final weapon.

"You do realize that our company gym is getting boring, right? Same people. Same routines. Same everything. Don’t you feel a little tired of it, hyung?"

Seungcheol had scoffed at the time, brushing it off with a lazy wave. But later that night, when he was back at the company gym, cycling through the same warm-ups, the same weights, the same sterile environment—he felt it.

That nagging sense of monotony.

And somehow, that was how he found himself standing outside a gym on the other side of town the following week, arms crossed, watching Mingyu practically bounce with excitement.

"See? It’s nice, right?" Mingyu beamed, swiping his membership card at the entrance. "And the people here are so chill, no one even looks twice at us!"

Seungcheol hummed noncommittally as he followed inside. The gym was… decent. Smaller than their company one, but the atmosphere was different. Cozy, like Mingyu had said. Warm lighting instead of the harsh fluorescents he was used to. A good mix of people—some regular gym-goers, others just there to stay active. No overly eager fans, no suffocating attention.

Alright, fine. Maybe Mingyu had a point.

"I'll give it a shot," Seungcheol finally muttered, rolling his shoulders.

"YES!" Mingyu fist-pumped like he had just won a bet.

–

This gym was never supposed to be a regular thing.

Originally, it was just a favor to Mingyu—a one-time visit, or so he thought. The younger member had insisted, claiming it was quieter than their company gym, had better equipment, and was “literally the perfect place to work out without distractions.”

"Just try it once, hyung," Mingyu had grinned, throwing an arm over his shoulder. "You’ll thank me later."

That never happened. But somehow, he kept coming back.

Not because of anything particularly special. He wasn’t someone who enjoyed changing up his routine. And yet, after that first visit, the place stuck in his mind.

It was quiet. No fans waiting outside, no cameras catching him off guard. The staff and members treated him like anyone else—just a guy coming in for a workout. No stares, no whispers.

It felt… normal.

And maybe that’s why his schedule started shifting around it.

At first, he only went when Mingyu was free. But, predictably, the younger man’s enthusiasm didn’t last long.

"Hyung, I can't today—early shoot."

"Hyung, let’s go tomorrow instead, I need sleep."

"Hyung, you’re still going? Damn."

One excuse after another, until he was going alone.

But stopping never crossed his mind. Somewhere along the way, this place had carved itself into his day, becoming as routine as practice or work. It wasn’t just about staying in shape anymore—it was about the rare stillness. A moment in his schedule that belonged to him.

And then, there was her.

It wasn’t immediate. No dramatic first meeting, no slow-motion glances across the gym.

She was just another regular at first. Someone who happened to be there at the same time.

Until she wasn’t just that anymore.

The little things started standing out. The way she always tied her hair back in a loose ponytail, strands slipping free by the end of her session. The way she scrolled through her phone between sets, completely lost in whatever she was reading. The way she carried herself—focused, steady, like nothing around her mattered.

Tuesdays. Thursdays. Fridays.

Always at the same time.

Always leaving just as he arrived.

He shouldn’t have cared about that.

But somehow, he did.

Because for someone he had never spoken to, who had never even looked his way—she was taking up space in his mind in a way he didn’t know how to stop

–

March, 2024

Seungcheol liked to believe he wasn’t easily distracted.

But lately, something had shifted.

It wasn’t the usual exhaustion from packed schedules or the weight of being SEVENTEEN’s leader. This was different—subtle, creeping in before he even realized it.

At first, it was just a passing thought. A brief glance at the clock before heading to the gym, an unconscious check to see if she was there.

Then, it became routine.

The moment he stepped inside, his eyes would instinctively scan the room, searching for a familiar figure. He told himself it was nothing—just habit, like any other part of his workout.

But on the days she wasn’t there, when the space felt a little emptier, a strange sense of disappointment settled in his chest.

Which made no sense.

He didn’t even know her.

She was just another gym-goer, part of the usual crowd.

And yet, habits were hard to break.

And once something—or someone—caught his attention, Seungcheol wasn’t the type to ignore it.

So, when he finally saw her up close for the first time, it hit him harder than expected.

The gym was quiet that afternoon, with only a few regulars scattered around. Seungcheol had just finished warming up when he turned—and there she was.

By the weights, adjusting her wrist wraps, completely focused on the task.

He shouldn’t have stared.

But something about the moment made it hard to look away.

Maybe it was the way she moved—calm, composed, lost in her own world. Maybe it was the way she carried herself, as if nothing could shake her.

Or maybe it was something else entirely.

Something he wasn’t ready to put into words.

He forced himself to look away, shaking off the thought.

Because that’s all it was.

A passing moment.

Nothing more.

At least, that’s what he told himself.

But the feeling lingered longer than it should have.

–

Obsession wasn’t in his nature. He was a leader, a decision-maker—someone who set goals and saw them through. But this? This was different.

The mystery of her lingered.

For weeks, she had been a presence just beyond his reach, slipping away before he could ever get close. Not once had they spoken, not once had he managed to be in the right place at the right time, yet somehow, she had taken up space in his thoughts.

And that wasn’t something he could ignore.

So, for the first time in a long time, curiosity got the better of him.

Answers weren’t hard to find—people talked, and the gym staff knew him well. A few casual questions here and there, nothing too obvious, and finally, he got what he wanted.

Her name.

Jang Sua.

He turned it over in his mind, testing how it sounded, how it felt. Simple, refined, carrying a quiet sort of confidence. It suited her.

And yet, the moment he had it, something about it tugged at him.

Familiar.

Like a name he had heard before but never really registered.

The realization didn’t hit him until later, when he was lounging in the practice room, half-listening to the others’ conversation.

Jang Sua.

Minghao’s Jang Sua.

The name that had surfaced in passing, always spoken with quiet admiration. The gallery girl, the art specialist—the one who had guided Minghao through paintings, pushed him beyond his comfort zone.

Recognition struck first. And then, something heavier. Something far more unsettling.

Minghao liked her.

Maybe not openly, maybe not in a way the others had picked up on, but now it was clear—the way Minghao’s voice shifted when he spoke about her, the way he lingered on details that had nothing to do with art.

And now, he wanted her too.

A slow exhale left his lips as he leaned back against the couch, eyes fixed on the ceiling.

Of course, it had to be her.

Because nothing was ever simple.

And walking away had never been his style.

—

“You look like you’ve got something on your mind,” Jeonghan mused, lazily swirling the straw in his iced americano.

Across from him, the man in question sat slumped in his chair, arms crossed, brows furrowed. It wasn’t like Seungcheol to be this quiet, especially during their late-night café runs. Normally, he was the one rambling about schedules, workouts, or whatever drama had unfolded in the group chat that day. But tonight? Silence.

Jeonghan smirked. “It’s a girl, isn’t it?”

The sharp exhale that followed was all the confirmation he needed.

“Not just any girl,” Jeonghan continued, amused. “It’s her, isn’t it? The gym girl you’ve been secretly obsessed with.”

At that, Seungcheol groaned, tilting his head back against the booth. “I’m not obsessed.”

“Sure. That’s why you’ve been going to the gym religiously every day at the same time, hoping to ‘accidentally’ run into her.”

He had nothing to say to that, so he took a slow sip of his drink instead.

Jeonghan leaned forward, resting his chin on his palm. “Alright, so what’s the problem? You like her. She doesn’t even know you exist. What’s stopping you?”

A beat of hesitation.

“…Minghao.”

That wiped the smirk off Jeonghan’s face. “Ah.”

Seungcheol exhaled, fingers tapping against his cup. “He likes her.”

There it was—the thing that had been gnawing at him for weeks now. Minghao wasn’t the type to wear his emotions on his sleeve, but it was painfully obvious. The way he talked about her, the subtle way his expression softened whenever her name came up… it didn’t take a genius to figure it out.

And yet, despite years of knowing her, he had never made a move.

“So let me get this straight.” Jeonghan sat back, tapping his fingers against the table. “Minghao’s liked her for years but never confessed, and now you like her too.”

Seungcheol nodded.

“And you’re debating whether or not to do something about it?”

Another nod.

Jeonghan let out a short laugh, shaking his head. “You know, for someone who acts all tough, you’re surprisingly considerate.”

Seungcheol scoffed. “Hannie.”

“Listen,” Jeonghan leaned in, voice low but firm, “if you make a move first and she chooses you, then that’s how it’s supposed to be. Minghao had years, Seungcheol. If he really wanted to be with her, he would’ve done something by now.”

That… was cruel.

But also true.

Seungcheol hated to admit it, but the thought had crossed his mind before. If Minghao was really that serious about her, why hadn’t he said anything? Why had he stayed in the safe zone all this time?

“You’re not doing anything wrong,” Jeonghan added, as if reading his thoughts. “You like her. You want to ask her out. That’s normal. What happens next? That’s up to her.”

The words settled in his chest, heavy but strangely reassuring.

He’d spent so much time hesitating, caught between his own feelings and the unspoken ones of his friend. But at the end of the day, the choice wasn’t his—or Minghao’s—to make.

It was hers.

And he was done waiting.

—

April, 2024

He never thought she'd say yes.

Even as the words left his mouth—carefully measured, laced with quiet hesitation—he had braced for rejection. He had prepared himself for the moment she would scoff, roll her eyes, maybe even look at him like he was out of his mind.

But she didn’t.

Instead, she tilted her head, studied him like she was searching for something beneath his careful composure, and then—"I’ll sign it."

And just like that, the ground beneath him shifted.

—

Dating Sua was unlike anything he had known before.

There were no grand declarations, no textbook romance gestures. She didn’t expect flowers or public displays of affection, didn’t demand more than what he could give.

Instead, she gave him something far more dangerous—a place to rest.

She never pried, never asked about things he wasn’t ready to share. Yet somehow, she always knew—when to let him be, when to tease him out of his exhaustion, when to lean against his shoulder and let the silence stretch comfortably between them.

Seungcheol had never met someone so effortlessly steady.

And he was already in too deep before he even realized he was falling.

—

The night it happened, he hadn’t planned for it.

They were at his apartment, the air thick with unspoken things. She sat on the couch in his hoodie, fingers wrapped around a cup of tea, looking so effortlessly like she belonged there that it made his chest ache.

Then, somewhere between soft laughter and quiet touches, she kissed him first.

It was barely there at first—a gentle press of lips, like she was testing something, waiting for him to stop her.

But he didn’t.

Instead, his hands found her waist, anchoring himself to her, deepening the kiss with a hunger he hadn't let himself acknowledge until now.

He felt her sigh against him, soft and warm, and something inside him broke.

It had been so long.

Too long since he let himself have this, let himself want without hesitation, without restraint.

And now, with her beneath him, her skin warm beneath his fingertips, her name a quiet prayer on his lips—he realized just how much he had missed this.

Missed her.

His hands trembled slightly as he traced the curve of her back, mapping the shivers he pulled from her, the soft gasps that sent heat curling through his veins.

"Are you okay?" she whispered, her fingers threading through his hair.

He exhaled a quiet laugh, pressing a kiss to the corner of her mouth. "Yeah." His voice was rougher than he expected. "You?"

She nodded, eyes heavy-lidded, lips swollen, beautiful.

And when he finally sank into her, when she breathed his name like it was something sacred—he knew.

There was no coming back from this.

—

After that night, it was over for him.

Seungcheol had always been careful—always kept a part of himself tucked away, guarded.

But now?

Now he was completely gone for her.

It was in the way he caught himself staring when she wasn’t looking. The way he found excuses to touch her, even in the smallest ways—a hand on the small of her back, fingers brushing hers, his thumb tracing absentminded circles against her skin.

The way he would wake up before her just to watch the slow rise and fall of her breath, to commit the softness of her to memory before the world pulled him away again.

He was in love with her.

So hopelessly, maddeningly in love with her that it scared him.

Because for the first time in a long time, he had something he couldn’t afford to lose.

—

August, 2024

Seungcheol had been careful.

At least, he thought he had been.

No one was supposed to know—not yet. Not until he figured out how to handle this properly. The moment the members found out, it would spread like wildfire. Not to the public, of course; he trusted them more than anyone. But within the group, between the teasing and the pestering, there would be no keeping it to himself.

So he had been careful. He had hidden it well. Or so he thought.

But now, as he sat in the dressing room, staring at the read receipt on his phone, he realized maybe he hadn’t been as subtle as he’d believed.

He had been smiling.

And someone had noticed.

"Who the hell is ‘Sua’?"

Seungcheol’s head jerked up.

Mingyu was standing over him, eyes locked onto his screen before he could react. He locked it immediately, but it was too late. DK was already launching himself onto the couch, eyes wide with betrayal.

"HYUNG, WHO IS SUA?? Secret girlfriend? Hidden manager? Are you being blackmailed? BLINK TWICE IF—"

"Mind your business," Seungcheol muttered, shoving him off, but his voice didn’t have enough bite.

Mingyu grinned, nudging his shoulder. “No, but really. Who is she?”

Seungcheol exhaled, pressing his tongue against the inside of his cheek.

"Someone important."

That should’ve been enough. That should’ve ended it.

But when he stood, stretching to make his escape, his gaze flickered across the room—

And there was Minghao.

Silent. Watching.

Seungcheol froze for a split second, just enough to feel the weight of Minghao’s gaze.

And then he turned away.

He knew that look.

Knew it too well.

Minghao had already figured it out.

—

Seungcheol wasn’t sure how long he had before Minghao confronted him, but he knew it was coming.

Minghao never reacted impulsively, never made a scene. He was careful, methodical, always waiting for the right moment to ask the right question.

So when the others had filtered out, leaving just the two of them backstage, Seungcheol didn’t need to turn around to know he was there.

"You’re seeing her."

It wasn’t a question.

Still, Seungcheol took his time turning. He could pretend to be surprised. He could play dumb. But there was no point.

Instead, he just met Minghao’s gaze.

"Yes."

Minghao didn’t flinch. Didn’t sigh. Didn’t react the way the others would have.

He just studied him.

"You never told me."

It wasn’t an accusation, but it wasn’t just a statement either. It held something else—something heavier, something that made Seungcheol’s stomach twist.

Because there was a truth underneath it.

You never told me.

But I told you about her.

I talked about her. I admired her. I trusted you.

And now, suddenly, she’s yours.

Seungcheol clenched his jaw, exhaling slowly. He could say I didn’t have to. He could say I didn’t think it mattered.

But both of those would be lies.

Minghao had noticed before anyone else. That was the kind of person he was—someone who paid attention, someone who saw things before they were spoken aloud. He had noticed the way Seungcheol lingered on his phone, the way his expression softened before locking the screen. He had noticed the flowers, the careful way Seungcheol crafted his words.

And now, standing in front of him, he wasn’t asking because he didn’t know.

He was asking because he wanted to know why.

Seungcheol swallowed. He could offer an excuse. Say it happened fast, that he didn’t want to make it a big deal. But none of those were true either.

He had avoided telling Minghao.

Because he knew it would feel like this.

Because he knew—deep down—that Minghao cared more than he ever let on.

And maybe that was the part that made Seungcheol feel guilty.

Minghao let out a quiet laugh, one that didn’t quite reach his eyes. “Just be careful, hyung.”

It wasn’t a warning. It wasn’t a threat.

It was a reminder.

Seungcheol didn’t ask what he meant.

Didn’t tell him that it was already too late for that.

—

September, 2024

It was supposed to be a casual night.

One of those rare evenings where practice ended early enough for them to grab drinks together, unwind after hours of sweating under bright lights and sharper critiques.

So here they were, packed into their usual spot—an upscale but quiet bar tucked away from prying eyes—nursing cold beers and emptying shared plates of anju.

Seungcheol had just returned from ordering another round when he felt it.

That shift in the air.

Subtle, but there.

The way the conversation slowed just slightly as he sat back down, the way glances flickered toward him—too fleeting to call out, but just enough to make his skin prickle.

And then—

“So,” Seungkwan began, slow, casual. A little too casual. “Sua, huh?”

Jun hummed, swirling his drink. “Interesting.”

"Very interesting,” Joshua echoed.

Seungcheol sighed, setting his glass down. “Just say it.”

Jeonghan, ever the executioner, leaned back with a lazy smirk. “We just realized something.”

A beat.

"She’s the same Jang Sua that Minghao always talks about."

Seungcheol barely reacted, years of self-control keeping his expression neutral.

But inside?

Inside, something twisted.

Of course, they figured it out.

He didn’t dare glance at Minghao, who sat a little too still, fingers resting lightly against his glass, gaze unreadable.

Vernon, unbothered as always, was the first to break the quiet. “Damn. Small world.”

“That’s one way to put it,” Woozi muttered.

DK, who always took a second longer to catch on, blinked. “Wait, so—” He turned to Minghao. “Isn’t she the one you always—”

“Drop it,” Minghao cut in smoothly.

The words weren’t sharp, but they carried weight.

DK shut up.

And just like that, the tension stretched taut.

Seungcheol breathed evenly, keeping his expression unreadable.

He didn’t owe anyone an explanation.

But under their scrutiny, he felt like he did.

Because he knew what they might thinking.

Was there something between them?Did she play them both?Did Minghao like her first?

It was bullshit.

Sua wasn’t like that.

And Minghao wasn’t the type to get strung along.

Seungcheol knew this.

And yet, the thought that even one of them might be entertaining the idea made his stomach coil uncomfortably.

He felt his jaw tighten, shoulders stiffening—

Then—

A soft nudge under the table.

Jeonghan.

Seungcheol turned slightly, catching the lazy way Jeonghan sipped his drink, the ever-knowing glint in his eyes.

“Cheol,” Jeonghan murmured, just loud enough for him to hear.

And just like that, the tension in Seungcheol’s body unraveled.

Because he knew what Jeonghan meant.

Let it go.

Starting an argument now would only make things worse.

So instead, Seungcheol exhaled. Forced himself to relax.

Shrugged.

“What can I say?” He reached for his beer, voice easy, light. “Guess Minghao has good taste.”

A beat.

Then—

Jeonghan snorted.

The others groaned.

And just like that, the weight in the air lifted.

Conversation picked up again, the scrutiny shifting elsewhere, and the moment passed.

Seungcheol took a slow sip of his drink.

Beside him, Minghao said nothing.

But Seungcheol didn’t miss the way his fingers curled around his glass just a little tighter.

──────────────────────────────

two chapters in a day bcs why not :)

[kendosticks]

@errorterror put an idea in my head. not sure if you were making a request or just throwing an idea out there, but the brainworms got hold of me anyway. warning: dumbassery abounds. ao3 link or below the cut

Paul Heyman has worked with monsters.

Champions. Legends. Men who maul and dominate and bend the industry to their will.

And now he’s here.

In a backstage lounge that smells like Lysol and catering-grade coffee, trying to broker a meeting between his two newest acquisitions. They know each other, sure, but not necessarily as allies, and both of them tend to be a bit…much, albeit in different ways. 

Seth is already waiting, cross-legged on the leather sofa. Sunglasses on, predictably, and nursing a plastic cup of overpriced cold brew teeming with lavender foam. He’s wearing a cropped jacket that’s somehow both entirely see-through and bulletproof, depending on the angle, and his nails are painted with little gold accents to match. 

He looks composed, if impatient. 

Polished.

Domesticated.

Paul is not fooled.

He remembers what Roman said once, barely looking up from lacing his boots.

“You know he's just a pampered little lapdog.”

And then Punk had expressed a similar sentiment recently—bitter, like it hurt to admit.

"That bitch'll roll over for anyone offering a belly rub.”

Paul had assumed they were exaggerating. Paul had assumed incorrectly.

In the short time that he and Seth have spent together post-Wrestlemania, Paul has been made aware of the fact that, perhaps, he has bitten off more than he can chew. Seth is everything that Punk and Roman implied, and then some. He comes with a list of instructions for care, typed up, printed out, and hand-delivered by Drew McIntyre. 

"He needs structure,” Drew had said. “And frequent verbal affirmation.”

Paul had laughed. It was not a joke.

Seth is a fucking nightmare to deal with on a personal level, but at least he possesses the pedigree of a champion. 

Paul doesn't hear footsteps. He hears the door slam. 

Bron arrives like someone fired him out of a cannon. Sweaty, t-shirt so tight it looks as if it's trying to rip itself off of his body out of fear, and a protein shake in one hand. 

Seth doesn't look up at first. Instead, he sniffs. Just a subtle twitch of his nose. He slides his sunglasses down and glances over the rim. 

Paul immediately feels a shift.

“Bron,” he starts cautiously. “This is Seth. Seth, Bron—”

“Yeah, Paul,” Seth says. “We've met.” 

“Right, well,” Paul clears his throat nervously. “We’re all aligned now. Unified. A new vision. Isn't that right?”

“You're late, by the way.” Seth's tone is clipped. He takes a sip of his coffee and licks the foam from his lip.

“You're…sparkly,” Bron says. He narrows his eyes. 

“Great, we're bonding. That's good.” Paul exhales.

Seth stands with the kind of practiced grace that makes Paul feel like he's watching someone prepare for a Best in Show showcase rather than a professional alliance. 

Bron cracks his neck. Seth takes a step forward. 

They are, Paul realizes with cold certainly, posturing. Seth's coffee is shoved into his hands and he scrambles to grab hold of the cup and keep it from spilling. Wouldn't that be a disaster?

Unburdened by his beverage, Seth drops to all fours without hesitation or a trace of irony. He sinks down, spine arched, lips curling, and growls. 

Bron’s nostrils flare. Then he barks. 

Not a laugh. An actual bark.

“Oh my god.” Paul's eyes go wide. 

They circle. One slow, taut loop.

Not like coworkers or allies.  No, it's as if they’ve been left unsupervised in a dog park and neither one knows who’s top of the pack yet.

This is not what Paul signed up for.

He used to manage Brock Lesnar, for god's sake! Who, despite being referred to as “the beast incarnate”, is very much a human. Not an actual beast or a…well, he’s not sure what Seth reminds him of. A golden retriever,  perhaps? An Afghan hound? Nothing comes to mind that fits his particular brand of beautiful but insane.  

Seth growls again low in his chest and Bron tilts his head like he’s trying to decide whether to bite or play.

Paul is afraid of both outcomes.

His mind seemingly made up, Bron lunges.

Not to maul, but to test. A quick snap of movement. A shoulder bump. Teeth not bared but visible.

Seth shoves back. Hard.

His nails scrape the floor. His lip curls. He pounces—not graceful this time, but fast, and lands on Bron with a thud that makes something rattle in the wall. Paul swears he hears someone in catering gasp.

They roll across the ground.

It’s not a fight, necessarily. It’s just…snarling, barking.... 

Oh god, mounting?

Paul is flabbergasted. His eyes dart away momentarily, horrified of what he might see next. 

Bron gets Seth onto his back for a second—just a second—but Seth is fucking unhinged. He twists like he’s done this a thousand times. His tight bun comes loose and curls shake free around his face. For everything he lacks in brute strength, he makes up for in strategy. 

He's scrappy, Paul has to give him that.

A blur of limbs, a snap of teeth near Bron’s throat, and then—Seth’s on top.

Straddling him with his head held high, radiating victory.

Bron goes still beneath him. He exhales begrudgingly like he knows the script and doesn't want to blow his cue.

Paul watches, frozen, as Seth barks a single, declarative bark and climbs off.

That's when Bron rolls over. Flat on his back, limbs loose, chin tilted just enough to expose his throat. 

It's submission. Well, technically.

Obviously, if Bron wanted it bad enough, this would've been over in seconds. He could've cracked Seth's ribs like a wishbone and walked away wagging his metaphorical tail.

He's holding back and playing along. Deep down, even if Bron doesn't understand the politics of all this, he knows what it means to be a Paul Heyman Guy, and apparently right now that title is worth losing a dogfight for. 

Paul lowers Seth’s coffee to the table with trembling hands.

“Oh my god,” he says again, softer this time.

Seth lifts his head, squares his shoulders and locks eyes with Paul. Not playful or pleased, just watching; a dog trained to sit and wait for its next command. He holds Paul in his gaze like he's evaluating a threat.

Paul swallows. 

He recognizes the look. It's the kind Roman has been known to give people before spearing them into next week. The kind Brock gave just before deciding someone didn't need a spine anymore. 

It's not rage. It's potential. That's good though, Paul can work with that. He wets his lips as panic creeps up his neck. 

“You were…” he stammers, “very—very good. Strong. Dominant. I mean that in the absolute best way possible, Seth.” He shrinks back slightly, as if bracing for an attack.

Seth sits back on his heels. He is satisfied. For now. 

“Great. Fantastic. I think we've made real progress.” Paul gives a strained smile and reaches into his jacket pocket for his phone. In his Notes app, he taps on Seth Rollins-Care & Handling. It already has seventeen bullet points—addendums to the guidelines he'd been given by Drew. He types in a few more:

Avoid prolonged eye contact during introductions.

Do not allow unsupervised interaction with large, untrained dogs.

He pauses. Then adds:

Praise immediately after displays of dominance. 

He hits save.

———

Now, they've settled.

Mostly.

Bron remains on the floor, stretched out like he's just finished a particularly satisfying workout. One shoe is off. His t-shirt is nowhere to be seen. There's a folding chair in the corner that's been dented, somehow. 

He's not growling anymore, but he’s breathing loud and occasionally flexing like he's about to pounce again, just for fun.

Seth is in Paul’s lap.

In. Not near. Not next to. In.

Head tucked under Paul’s chin, breathing slow and warm against his neck. Paul wrinkles his nose at the sensation. His arm is around Seth purely for containment purposes.

He strokes Seth’s hair because that seems to keep the fussing to a minimum.

“Thank you for not biting him,” Paul mutters.

Seth hums.

“I can be good,” he says.

Paul doesn’t answer. 

He studies Bron. There's no challenge in his eyes. Not yet. 

But Paul knows how fast that could change. If it does, well, he'll be ready.

He used to work with monsters.

[collapsedsquid]

An international scientific competition widely credited with spurring the development of artificial intelligence (AI) for biology appears to be on its deathbed. Known as the Critical Assessment of protein Structure Prediction (CASP), the 3-decade-old competition has run out of funding from the U.S. National Institutes of Health (NIH) and will exhaust emergency support from the University of California (UC) Davis, which oversees the grant, on 8 August. UC Davis has told the two researchers who run the program that their jobs will end in weeks. NIH officials have offered no reassurance about the program’s future, despite repeated inquiries from CASP organizers, who submitted a request to renew their $800,000 grant last year. The agency did not respond to multiple requests for comment. John Moult, a CASP co-founder at the University of Maryland, says contest organizers are “scrambling” to find alternative funding from foundations and other countries.

[overly-hubristic-mad-scientist]

I think with AI we kinda lost the plot, why am I always being advertised for another shitty generative AI that does basic shit any person can do themselves. No I don’t want to us AI to make a shopping list. Idk I think we should relegate that stuff to like, machine learning to predict protein structures or identifying cancer cells and stuff like that please

[bpod-bpod]

Going for Fold

For generations, scientists have struggled to follow the steps that shape life. Alphafold, a project that recently won the 2024 Nobel Prize in Chemistry, may be a giant leap ahead. Researchers use artificial intelligence to predict how proteins – the tiny machines with specific shapes set to tasks inside our cells – take shape from their amino acid building blocks. Similar perhaps to predicting a castle, pirate ship or bunch of flowers from a pile of Lego bricks (although ~100 million times smaller), at least the algorithms have some rules to guide them. Here they simulate the natural steps of protein synthesis – taking a virtual chain of amino acids and folding it up based on how different amino acids interact chemically. Researchers believe this predicted protein protects the malaria-carrying parasite Plasmodium falciparum from our immune defences. The next step is to scour the 3D structure for weaknesses, while Alphafold continues its predictions.

Written by John Ankers

Image from the AlphaFold Protein Structure Database

EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire and Google DeepMind, London, UK

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Research referenced published in Nature Communications, May 2024

You can also follow BPoD on Instagram, Twitter, Facebook and Bluesky

[felixcloud6288]

My last project for this semester is for a multimedia databases class and it's a simple "Pick three recent papers that are relevant to this class and have a shared topic and write a summary of them". Since I'm in bioinformatics, I decided to use this as an opportunity to read up on protein folding methods, and I have gotten bizarrely obsessive about explaining everything I can about the papers I chose.

I wrote a whole page just going over the Critical Assessment of Structure Prediction (CASP) that's used to measure the accuracy of protein folding tools, and set aside a whole section in the first paper summary where I gave a brief explanation about certain types of protein folds.

I'm making this post because I realized two of the papers I'm using are from the same author and I just emailed them to ask for a comment on why one of the tools they made is no longer available. I'm assuming it's because the later tool they made makes the older one obsolete, but I want to get confirmation before I say anything.

[thoughtportal]

June 5, 2025

The velvet worm, a squishy little predator that looks like the stretch-limo version of a caterpillar, has a whimsical MO: it administers death by Silly String.

In the leaf litter of tropical and temperate forests around the world, velvet worms stalk the night on dozens of stubby legs. The pocket-size predator—whose species range from less than half an inch to eight inches long—can barely see, so it bumbles around, hoping to literally bump into an edible bug such as a cricket or a woodlouse. When it finds one, the velvet worm uses nozzles on either side of its face to shoot jets of sticky slime at its victim.

“It happens so fast it’s almost like they’re sneezing,” says Matthew Harrington, a biochemist at McGill University who has studied velvet worms for a decade.

At first, the goo is a watery liquid, but in midair it transforms into jellylike ropes that ensnare the unlucky creature and stick it to the ground. As the prey struggles, the slime forms fibrous threads, and within seconds the substance hardens into a glasslike solid.

Scientists have been intrigued by velvet worm slime’s adhesive properties for more than a century. (In the 1870s researchers puzzling over what makes it stick tried tasting it. The verdict: bitter.) Recent findings suggest the phase-shifting goo could inspire a new generation of recyclable bioplastics, according to research published by Harrington and his colleagues in the Proceedings of the National Academy of Sciences USA.

Previously, the researchers discovered that soaking the hardened fibers in water returned them to their liquid state—and by rubbing the resultant mess between their fingertips, they could get fibers as strong as nylon to re-form. That means “everything we need to know about making these fibers is encoded in the proteins themselves,” Harrington says.

But isolating those proteins is easier said than done, the scientists found. The slime is so sensitive to touch that even standard laboratory techniques such as pipetting can trigger its phase shift. To avoid that sticky situation altogether, the scientists sequenced the RNA of proteins from the slime of velvet worms collected in Barbados, Singapore and Australia. Then they fed the RNA sequences into AlphaFold3, a program that uses artificial intelligence to predict protein shapes. For all three species, it “spit out this horseshoe shape” rich in the amino acid leucine, Harrington says.

Although this structure is novel to materials scientists, it’s old hat to evolution. A similar protein called a toll-like receptor is part of an ancient immune system feature found across plants, invertebrates and vertebrates. These receptors sit on the surface of immune cells, binding tightly to pieces of invading microbes and releasing them later. Harrington and his team suggest the horseshoe-shaped protein may use a similar “host-guest” dynamic to grab onto other proteins in the slime, binding strongly but reversibly to form the powerful fibers. Those are magic words to materials scientists working on developing replacements for plastic that can be broken down easily and re-formed into new shapes.

These horseshoe proteins are a significant find, says Yendry Corrales Ureña, a researcher at Costa Rica’s National Laboratory of Nanotechnology who studies velvet worm slime but wasn’t involved in the study. She adds, however, that these proteins don’t account for important properties of the slime such as its toughness or elasticity. “They are just one piece of the larger puzzle.”

Julian Monge Najera, an ecologist at the University of Costa Rica who researches invertebrate evolution, says the fact that three velvet worm species from different continents have the same protein shape in their slime underscores how incredibly ancient velvet worms are and how long ago their chemical R&D must have occurred.

The fossil record shows that velvet worms have existed almost exactly as they do now for at least 300 million years, predating both dinosaurs and today’s continents. “If I could go back in a time machine, the velvet worms I would catch in the post-Cambrian period would be identical to the ones in Costa Rica’s cloud forests today,” Monge Najera says—phase-shifting slime and all.

Harrington and his team are working to purify the horseshoe protein from the slime and confirm its structure via electron microscopy. “We won’t be milking velvet worms for slime to replace plastics,” Harrington says. “But we hope to copy their chemical tricks.”

[justgivemethephd]

17.02.2025

Happy Monday everyone!

Starting off the week very strong, and even though I am incredibly low energy I managed to get a lot done. A lot of admin sorted first thing in the morning since that’s the thing I least wanted to work on, immediately followed by a lecture and hours of reading so I can understand the principles of protein structure prediction and the way this program I want to use works. For me, there’s just no point in using a tool if I can’t explain how it generated the data or how to interpret the results. I also did some cell culture work, but honestly the reading took up the majority of the day and gave me such a headache. Still, I think after tomorrow I’ll definitely crack it!

The rest of the week will involve a lot of computer analysis and a few workshops, but I’m still very much looking forward to my lab work. I’m doing some in vitro digestions and I know the results for that would look amazing if everything works! I can’t wait to see it.

I also smashed my training today! I was so excited to go to the gym, and managed to run 5km in 30 mins! I’ve never managed to maintain 10km/h for that long, and even though I had to take a 1min break after 20mins of running it felt so amazing to see how far I could push myself without injury. It was definitely hard, but it was so rewarding.

Let’s push ourselves this week guys!!!

_____

🎧 - Lotta True Crime by Penelope Scott

🎮 - Baldur’s Gate 3

📖 - Onyx Storm by Rebecca Yarros

[kamounlab]

Workshop: AI-guided structural modelling workshop: Genomes to structures; Al-Ain, UAE, Tuesday, May 2025

Join us for a hands-on workshop on AI-guided structural modelling - from genomes to protein structures! This workshop covers theoretical and practical aspects of AlphaFold, including predicting monomers, protein complexes, and ligand interactions. Learn to visualize and interpret AlphaFold outputs using ChimeraX, perform structural alignments, and leverage tools like Foldseek, TM-align, and FoldMason. We’ll discuss the advantages and limitations of these cutting-edge tools, highlighting how structural predictions can drive hypothesis generation and experimental design. While illustrated with examples from plant host-pathogen interactions, the insights and skills gained here will be broadly applicable to diverse research fields.

Thanks to Andy Posbeykian, Yu Sugihara, James Canham @GetGenome and the Team at Khalifa Center for Genetic Engineering and Biotechnology.