Akshat Nigam

💥 Drug discovery software is broken
Customers pay big fees for tools that may not work

👉🏽 We started KlyneAI to build tailored tools for your challenges—not generic ones

No sugar-coating. If it doesn’t work, we stop—you don’t waste money.Time for an honest, problem-driven approach to drug discovery

Hot take in drug discovery: The real value of molecular docking lies in ranking for (ultra-large) virtual screening.

Structure co-folding models with ligands? Super cool! But unless they prove themselves in screening performance, conventional docking still wins 🤔

🚀 Big news from Klyne!

We’re thrilled to be collaborating with @cgorgulla.bsky.social ky.social's lab to develop the next generation of tools for accelerating drug discovery.

Stay tuned—some exciting papers are on the way from this collaboration!

‘Living proof that you can spend money on the poor’: Utopia comes to Mexico City A visionary mayor has harnessed her imagination to promote health, wellbeing and culture in one of the Mexican capital’s most impoverished neighbourhoods

More of this. Please.

www.theguardian.com/global-devel...

🚀 Exciting News! 🚀

KlyneAI is thrilled to join JLABS! We’re pushing the boundaries of biotech innovation and developing cutting-edge tools for drug discovery.

Want to collaborate on AI-driven drug discovery?
→ klyne@klyne.ai

#Biotech #DrugDiscovery #AI #JLabs

(Yes, the view’s amazing) 🤩

Registration for the 2025 Accelerate conference in Toronto (Aug 11–14) opens soon! Be the first to know: zr2z766pxls.typeform.com/accelerate25

In our recent publication, we describe a systematic framework leveraging the documentation of the quantum chemistry suite ORCA for developing large language models that are capable of providing input files based on user prompts with the help of prompt engineering, retrieval-augmented generation […]

Absolutely love working with @aspuru.bsky.social 😁

Check out this great interview with the incredible @aspuru.bsky.social on BNNBloomberg, highlighting a recent publication co-authored by our CTO,
@akshatai.bsky.social ! [Paper: rdcu.be/d68Fs]

Exciting times ahead for Klyne—stay tuned for more! 🚀🔬

t.co/tkLsgjcSDb

On a separate note: @klyneai.bsky.social develops practical, affordable software for drug discovery! Reach out at [akshat@klyne.ai]. Our team supports all stages with a pay-as-you-go model, no licensing fees, and costs nearly an order of magnitude lower than competitors—while maintaining quality 😊

Happy to answer any questions about this! 🚀

A pleasure working with so many awesome people @Mohammad Ghazi Vakili, @cgorgulla.bsky.social , @aspuru.bsky.social, Igor Stagljar & @elonverse.bsky.social e.bsky.social & so many more!

3️⃣ What’s next? This is just the beginning. Generative models have immense potential to accelerate drug discovery. Future work will explore larger quantum systems and transformer-based models. Though not yet practical, advancements in quantum technologies will greatly enhance their impact.

2️⃣ Quantum vs. classical approaches: Could classical methods achieve similar results (e.g., Tartarus benchmarking)? Probably—but we observed something fascinating. More qubits in the quantum model improved its ability to generate stable, synthesizable molecules, suggesting better distb. modeling:

1️⃣ Early-stage inhibitors, not yet drugs: The inhibitors we identified are still in the early stages of development—not ready to be called "drugs." However, this work demonstrates the potential of quantum generative models in molecule design and their applicability in real-world scenarios.

Excited to share our latest work, published this morning in Nature Biotechnology! 🎉 We developed a hybrid quantum computing-enhanced generative model to design KRAS inhibitors. Check it out here: rdcu.be/d68Fs.

Some fascinating insights along the way:

Thrilled to welcome @akshatai.bsky.social to Klyne! 🚀

Stay tuned for exciting science updates. Have biotech questions or needs? We're here to help: klyne@klyne.ai

Excited to share some news this New Year! I’ll be joining @klyneai.bsky.social as CTO soon.

We co-founded Klyne to revolutionize biotech with cost-effective, no-licensing-fee software solutions. 🚀

If you're interested in screening, hit optimization, or FEP calculations, reach out: klyne@klyne.ai 😉

Inverse design of copolymers including stoichiometry and chain architecture The demand for innovative synthetic polymers with improved properties is high, but their structural complexity and vast design space hinder rapid discovery. Machine learning-guided molecular design is a promising approach to accelerate polymer discovery. However, the scarcity of labeled polymer data and the

#RobSelects paper of the week #ChemicalScience: Variational autoencoder for property-directed inverse design of organic copolymers. #aichem https://doi.org/10.1039/D4SC05900J

In biomolecular simulations, interesting phenomena often unfold slowly, with the viscosity of the surrounding water further hindering conformational sampling.

But what if we could simulate water with lower viscosity while preserving the same thermodynamic properties?

👇

4️⃣ Quantum computing + KRAS inhibitors: arxiv.org/abs/2402.08210

Full list of publications: scholar.google.com/citations?hl...

Huge thanks to my advisors, mentors & collaborators for their support! 🚀 #PhDDefense #Stanford #MachineLearning

1️⃣ Designing transcriptional repressors with deep learning: biorxiv.org/content/10.1...
2️⃣ VirtualFlow 2.0: Screening 69B molecules: biorxiv.org/content/10.1...
3️⃣ Tartarus: Benchmarking inverse molecular design: proceedings.neurips.cc/paper_files/...

🎉 Thrilled to share that I’ve successfully defended my PhD @Stanford! My thesis, "Machine Learning Approaches for Predicting Biological Function and Molecular Design," explores the intersection of ML, biology, and chemistry.

Some Highlights:

Thank you Martin! 🙂

Thanks Kjell! 😄

Thanks @anshulkundaje.bsky.social! Really appreciate all the support in my PhD from both my advisors 🙂

Surprised by how much of the scientific community has moved here—seeing so much more scientific content and a big boost in post quality here! Looking forward to posting more here! 😉