Idris

A young man interested in biology and bioinformatics

[ToposBio @ToposBio]

Today we are announcing Topos-2, our next-generation model for generating the full range of shapes a protein can take, across the order-disorder spectrum.

We are also previewing Topos-Bind: to our knowledge, the first generative model to capture the range of shapes for disordered proteins bound to small molecules.

Read the technical blog post here: https://t.co/BLAXHAgsH4

(1/7)

[Silvi Rouskin @silvirouskin]

Ok let me explain how cool this is from my perspective , please RT! I developed one of the first methods to probe RNA structure in high throughput inside living cells, and it takes tons of time and $$ to apply on thousands of viruses - it’s practically impossible. This ML approach is just as good and works in seconds for nearly free ! Not only that, it highlights the MOST IMPORTANT structures that track with function. It’s the future of RNA strucute prediction and discovery across all families 🔥 https://t.co/aAJOXI7xrN

[Romero lab @romerolab1]

Have you ever wanted to talk to your molecules? Now you can with Chat with PyMOL!

We built this in the Romero Lab to make PyMOL more accessible to our BME undergrads, but quickly found it’s simply a better way to interact with molecular structures. (1/2)

[Kazuhiro Maeshima @kazu_maeshima]

Is euchromatin really “open”? 🧬 Using super-resolution imaging🔬 our new study @NatureGenet reveals: Euchromatin forms condensed domains in live cells. Cohesin constrains them and prevents domain mixing for proper transcriptional insulation���� 🔗https://t.co/HjjYOjycld (1/2)

[Idris @Edrees_Adl]

It is sad that as Africans and Arabs we are not included when China speaks in those terms
We are among nations that most support China

[Polymarket @Polymarket]

JUST IN: Xi Jinping invites 100,000 young Americans to study in China over the next 5 years to experience “the great rejuvenation of the Chinese nation.”

[Idris @Edrees_Adl]

@tsvenusrosie international student you don't take Gaokao You take the CSCA exam which is available in English as universities don't mind if you don't know Chinese yet However you will still need a foundation year to learn Chinese since most degree programs are taught in it

[Minkyu Jeon @MinkyuJeon19791]

Excited to share T-REX 🦖: Target-adaptive Rescue-Explore-eXploit, an agentic campaign controller for high-throughput de novo protein binder design!

T-REX treats protein design as an online agentic allocation problem to leverage diverse tools with efficient GPU usage 🧵

[Martin Pacesa @MartinPacesa]

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use.

We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition.
https://t.co/O8pr6jH99t

[Ah-Ram Kim @ahramkim1128]

🚀 New tool out! LIVIA (Local Interaction Visualization and Analysis) — a browser-based tool for assessing and visualizing predicted protein-protein interactions.

Drop in a prediction from AlphaFold-Multimer, AF3, ColabFold, Boltz-1/2, Chai-1, or OpenFold3 (ZIP or folder, auto-detected) and LIVIA answers the two questions you actually care about:

▸ Do these proteins interact?
▸ Which residues form the interface?

What you get:
▸ Interface confidence scores — iLIS (our local metric), ipSAE, actifpTM, ipTM
▸ Interaction interface heatmaps (PAE, LIS, cLIS)
▸ Sequence viewer + linear & circular contact maps highlighting Local Interaction Residues (LIR) and contact LIR (cLIR)
▸ Embedded Mol* 3D viewer
▸ Downloadable ChimeraX & PyMOL scripts

Also fetches dimers directly from the AlphaFold Database — adding the interface annotations AFDB doesn't provide.

Everything runs locally in your browser. No install, no upload.

LIVIA started as a personal tool — I built it with Claude Code and used it to make every structure figure in our FlyPredictome preprint (Kim et al., 2026). (Claude Code is truly insane...) Along the way I realized it could be useful for others, too.

If you have a favorite color palette for structure visualization, please let me know — happy to add it as a preset 🎨

🔗 LIVIA tool: https://t.co/qSaedW3yka
🐍 iLIS / batch CLI: https://t.co/jYN3yg3l6a
📄 LIVIA preprint: https://t.co/uHwEbAMBGH
📄 FlyPredictome preprint: https://t.co/O3mAOzF2GD

[Adwoa @AdwoaBiotech]

Let’s circle right back to the genesis of this bioinformatics journey.

B4 analysing anything, the 1st job is to confirm that the files you received are identical to the files that left the sequencing instrument.

1/The usual way to do this is with a something called a checksum.

[Idris @Edrees_Adl]

@MericaCulture Regarding the era of Italian colonization of Libya I call it the era of bringing civilization.
An Italian government presence was established in my country with the opening of the first anti slavery and slave liberation organization named The Italian Anti-Slavery Society

[Idris @Edrees_Adl]

@robthrills @DrewPavlou There are genuinely persecuted people who could become grateful contributors to Europ societies that treated them as human beings The tragedy is that those with money and connections to escape are often the sons of warlords and corrupt elites rather than most deserving of refuge

[Sergey Ovchinnikov @sokrypton]

ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim, Martin Steinegger, Milot Mirdita

🐍 pip install colabfold[alphafold]

(1/3)

[Adwoa @AdwoaBiotech]

1/
 Ok, actually running HISAT2 now instead of just talking about it.

Step-by-step, with commentary, because apparently I can't do anything without commentary.

[Structure @Structure_CP]

Online now! AlphaBridge: Tools for the analysis of predicted biomolecular complexes https://t.co/SNo3R7cwnv

[César de la Fuente @delafuentelab]

What if peptide design could become programmable?

Excited to share our new OmegAMP preprint, where we explore a step toward moving generative AI from simply producing candidate molecules to designing peptides with controllable properties and functions.

OmegAMP enables control over fundamental physicochemical properties (including length, charge, and hydrophobicity) while also supporting analog and motif-guided design. We experimentally characterized 204 peptides, identifying potent antimicrobials, multifunctional molecules, and lead designs with in vivo efficacy against A. baumannii.

The broader goal is to make molecular design increasingly precise and controllable: using machines not only to discover biological function, but to help us understand and engineer it for human health.

Grateful for a wonderful interdisciplinary collaboration with @szymczak_pau, @mdt_torres, Diogo Soares, @leon_het, Bruno Puczko-Szymański, Stefanie Jegelka, @guennemann, @fabian_theis, @ewa_szczurek, and our colleagues across @CompHealthMuc, @HelmholtzMunich, @TU_Muenchen, @MunichCenterML, @MdsiTum, @WydzialMIMUW, @Penn, @CBE_Penn, @PennBioeng, @PennEngineers, @PennMedicine, @PennChemistry, @PennMicro, @PennPsych, and @PennSAS.

Link to paper: https://t.co/rubiir9Clw

[Nayoung Kim @__na__young__]

1/8 💎 Introducing Packora: a state-of-the-art generative model for molecular crystal structure prediction (CSP).

🧩 Flexible, optional conditioning
🏆 Two-track evaluation + leading performance
🔬 Extensive, systematic ablations

[Idris @Edrees_Adl]

@andrewaiginin I don't know why I always remember this novel whenever I see someone doing something with that fly
Everything a novel's villain has done to human beings, they did to that fly.

[Idris @Edrees_Adl]

@OkojiAmarachukw All the leaders of this continent are like this If only Europe would expel them seize their money or imprison them. But a big part of the problem is our own people living in Europe who accept humiliation and European pity but will not fight these corrupt leaders.

[Jake Wintermute 🧬/acc @SynBio1]

I accept my fate