Ahmet Sarigun

Ahmet Sarigun

@asarigun.bsky.social

curious explorer - https://asarigun.github.io/

30 followers106 following8 posts

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Ahmet Sarigun
@asarigun.bsky.social

I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method. Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating... Thread - (1/n)

Ahmet Sarigun reposted

Ahmet Sureyya Rifaioglu
@ahmetrifaioglu.bsky.social

🎉 Happy to share our new work SpaCEy, now available🧬 SpaCEy is an explainable method for learning clinically relevant spatial tissue organization directly from spatial omics data—without predefined cell types or regions. 📄 Paper: www.biorxiv.org/content/10.6... 💻 Code repo: github.com/saezlab/SpaCEy

biorxiv.orgbiorxiv.org
Saez-Rodriguez Group@saezlab.bsky.social

See 👇 our new manuscript introducing SpaCEy, an explainable method for predicting clinical outcomes from spatial omics data 🧬 📄 Paper: www.biorxiv.org/content/10.6... 💻 Code repo: github.com/saezlab/SpaCEy

Ahmet Sarigun reposted

Matthieu da Costa
@mdc-biocat.bsky.social

With the release of Boltz 2, is there already a review comparing the efficiency of different (new) docking tools? (I’ve already tried Pocket Vina, which is actually quite good for high-throughput)

Ahmet Sarigun reposted

Radoslav Krivak
@rdkbio.bsky.social

🚀 GPU-accelerated docking to P2Rank-predicted pockets

Ahmet Sarigun@asarigun.bsky.social

I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method. Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating... Thread - (1/n)

Ahmet Sarigun
@asarigun.bsky.social

I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method. Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating... Thread - (1/n)

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Ahmet Sarigun
@asarigun.bsky.social

We benchmarked PocketVina across four widely used datasets (PDBbind, PoseBusters, Astex, DockGen), and introduce TargetDock-AI — a large-scale benchmark of >500K protein–ligand pairs with activity labels from PubChem. (5/n)

Ahmet Sarigun
@asarigun.bsky.social

All results, code (MIT License), and data are open and available: 📄 Paper: arxiv.org/abs/2506.20043 📦 Data: zenodo.org/records/1573... 💻 Code: github.com/BIMSBbioinfo... Huge thanks to co-authors @al2na.bsky.social, @borauyar.bsky.social, and Vedran Franke!

arxiv.orgPocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket ConditioningSampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-effic...
Ahmet Sarigun
@asarigun.bsky.social

I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method. Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating... Thread - (1/n)

View full thread
Ahmet Sarigun
@asarigun.bsky.social

PocketVina offers a robust alternative: • Identifies multiple pocket centers using P2Rank • Performs GPU-accelerated docking with QuickVina 2-GPU 2.1 • Completes docking + binding affinity prediction in under 1.5 seconds, with no model training (3/n)

Ahmet Sarigun
@asarigun.bsky.social

I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method. Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating... Thread - (1/n)

Ahmet Sarigun reposted

Leif S. Ludwig
@leifludwig.bsky.social

Join us to connect with the vibrant #singlecell community. 📢Register for the #ISCO'25 Conference "Innovations in #SingleCell #OMICS" in Berlin! 🗓️ 12-13 May 2025 🎤 Fantastic Keynote and Invited Speakers 🫵🏿 Many slots for talks: submit your abstract 🔗http://isco-conference.eu Please spread the word!

Ahmet Sarigun reposted

Pia Rautenstrauch
@prauten.bsky.social

1/4 🧵 Preprint alert: In "Metrics Matter: Why We Need to Stop Using Silhouette in #SingleCell #Benchmarking," we reveal critical flaws in common #Evaluation metrics for #Integration and propose robust alternatives. @uweohler.bsky.social www.biorxiv.org/content/10.1...

biorxiv.orgMetrics Matter: Why We Need to Stop Using Silhouette in Single-Cell BenchmarkingCurrent-day single-cell studies comprise complex data sets affected by nested batch effects caused by technical and biological factors, relying on advanced integration methods. Silhouette is an establ...

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