@Edrees_Adl

A young man interested in biology and bioinformatics

Joined January 2022
  • Tweets908
  • Following1K
  • Followers148
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It’s the law of the desert unless you are wealthy or from a Western country your life means nothing to them.
Sana Yousafzai@SanaYousafzai9Oct 19
A Bangladeshi couple sentenced to death in Saudi Arabia did not commit murder, theft or adultery. Their crime was simply kissing, an act that Cristiano Ronaldo has engaged in repeatedly on Saudi soil. This raises serious questions about fairness, justice and double standards. 💔
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Today we are excited to release Artios, a fully open source system for designing functional de novo enzymes. Enzymes present a new frontier for de novo protein design models due to the challenge of coordinating precise chemistry, rather than binding a target. Enzymes are life’s biological machines and by designing them we can truly start to engineer biology. We believe these fundamental capabilities should be built in the open and shared with the community to progress science faster. 🧵 1/6
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A single mutation or PTM can determine whether two proteins bind. But how can we predict binding specificity if our data lose those details? 🥺 Introducing SNOOPPI, a Sequence-Normalized database of On- and Off-target PPIs, now out at #Bioinformatics! 🐶 📜: doi.org/10.1093/bioinformati… 🤗: huggingface.co/datasets/Chat…
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Chens@Chensss_JOct 20
Excited to share what we’ve been building with Chaperone! In our benchmark, Chaperone reduced token usage by 86%. We also went from hypothesis to sequences ready for wet-lab testing in just two weeks—yielding a 1.32 nM cortisol binder in the first experimental round!
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Public preview of BioEmu2! @MSFTResearch AI for Science’s new foundation model for biomolecular structure, dynamics and function. Open weights, MIT license. github.com/microsoft/bioemu2 Movie: BioEmu2-simulated binding of intrinsically disordered peptide PUMA to MCL-1 receptor. 🧵⬇️
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Idris retweeted
subseq.bio
@subseqbio10h
BioEmu2 is now available on web, API, and MCP! Equilibrium ensemble sampling for proteins, nucleic acids & ligands — up to ~1,000,000× faster than traditional md simulation github.com/microsoft/bioemu2
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✨Introducing Prompteina: all-atom protein design directly from natural language✨ - Control diverse protein properties through a single text prompt - Higher predicted binding confidence than baselines - First experimentally validated de novo binders reported for GM2A 🧵
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酵素反応機構解析ツールpdb2reactionの論文がACS Omegaに掲載されました！ pubs.acs.org/acsodf/article/… PDB等の複合体構造から、活性部位モデル構築→MEP探索→TS最適化→IRC→熱化学までの反応機構解析を、機械学習ポテンシャルを用いてend-to-endで実行できます。 GitHub: github.com/t-0hmura/pdb2reac…
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"Simplifying in silico protein evolution with minimal screening by unZipro" Qin Z ∙ Zhao S ∙ Deng Z ∙ Si X [..] Chen Z ∙ Song J ∙ Wang D ∙ Ji X. Mol Cell. 2026-09-24. doi.org/10.1016/j.molcel.202… unZipro (unsupervised Zero-shot inverse folding framework for protein evolution) Testing fewer than ten nominated candidates (incl. AlphaFold3 model) identifies high-fitness variants #CRISPR #BE #PE #Plant_breeding
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Idris retweeted
ToposBio
@ToposBioSep 30
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: toposbio.ai/topos-2-topos-bi… (1/7)
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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 🔥 biorxiv.org/content/10.64898…
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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)
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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🚧 🔗nature.com/articles/s41588-0… (1/2)
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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
@PolymarketSep 24
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.”
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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 🧵
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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. github.com/PacesaLab/BindCra…
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🚀 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: flyark.github.io/LIVIA 🐍 iLIS / batch CLI: github.com/flyark/AFM-LIS 📄 LIVIA preprint: biorxiv.org/content/10.64898… 📄 FlyPredictome preprint: biorxiv.org/content/10.64898…
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Idris retweeted
Adwoa@AdwoaBiotechSep 18
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.
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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)
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Adwoa@AdwoaBiotechSep 16
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.
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