Adam Pecina

Interesting graph, @lindorfflarsen.bsky.social! I guess what is not captured here are the potential revenues from successful exits of university spin-offs. I would assume universities usually keep some equity in those companies, right? Are there any data on equity shares of Universities?

Our #CECAM Flagship Workshop brought together leading minds from academia & industry to push the boundaries of #QM, #ML & #MD in #DrugDesign.

Big thanks to @cecamevents.bsky.social @iocbprague.bsky.social @iocbtech.bsky.social & to all participants for the energy & insights!

#compchem #SQM

Final sessions at our #CECAM Workshop featured Lance Westerhoff, Peter Nagy & Subrahmanyam Sappati on QM/MM refinement, high-level #QM benchmarking & antifungal design. A strong finish with lively discussions & closing remarks!

@cecamevents.bsky.social
#CECAMinPrague @iocbprague.bsky.social

Day 3 opened with Kenneth Atz @Roche tackling the holy grail of #CADD: P-L binding #affinity prediction. By reframing limits of data & models, we can focus on the next solvable challenges - a sharp reminder of complexity & progress ahead.
#CECAM @cecamevents.bsky.social @iocbprague.bsky.social

Closing Day2 with exciting talks:
M.Lepsik on #SQM scoring on AI-generated structures,M.Hennemann on local properties at P-L interfaces & I.Gordiy on enhanced sampling with ML potentials.Inspiring end before our social dinner!
@cecamevents.bsky.social @iocbprague.bsky.social @iocbtech.bsky.social

This afternoon at our @cecamevents.bsky.social Workshop in Prague:
Talks by Ulf Ryde, Ran Friedman & Charles-Alexandre Mattelaer explored QM methods for binding affinity, energy decomposition & binding geometries. Great discussions on rigorous QM in drug design!
#compchem @iocbprague.bsky.social

Morning session of our #CECAM Workshop in Prague featured @gdefabritiis.bsky.social presenting a ML force field for drug discovery, Julien Michel on electrostatic embedding for ML/MM free energy calcs, and Carlos Cruz Marin on ML models for logP.
@iocbprague.bsky.social @cecamevents.bsky.social

We opened Day 2 of our #CECAM flagship workshop in Prague with the CECAM director Andrea Cavalli, highlighting steered #MD, dynamical docking & the complexity of binding energetics, and the challenges ahead. 🚀

#CECAMinPrague @iocbprague.bsky.social @cecamevents.bsky.social @iocbtech.bsky.social

You are greatly missed here Oles! Hope all went well on your side and meet you next time!

#cecam #cecam #quantumchemistry #drugdesign #machinelearning #cecam #iocb #sqm #cecaminprague #compchem | Adam Pecina The afternoon of Day 1 at the #CECAM Flagship Workshop “Quantum Chemistry for Drug Design: From Theory to Applications” in Prague continued with a great line-up of talks. Andreas Göller shared experi...

www.linkedin.com/posts/adampe...

Day 1 of our #CECAM Flagship Workshop in Prague started strong!
Talks by Kennie Merz, Jan Řezáč, Markus Hermann & Hamza Ibrahim sparked great discussion on #QM, #ML & #DrugDesign

Thanks to @iocbprague.bsky.social, @iocbtech.bsky.social & @cecamevents.bsky.social for support!

#compchem #SQM

Tomorrow we kick off our #CECAM Flagship Workshop on Quantum Chemistry for Drug Design (Sept 8–10, Prague). 3 days of cutting-edge talks bridging #QM #ML & #drugdesign with world-class speakers shorturl.at/5sooU

#compchem #SQM @iocbtech.bsky.social @cecamevents.bsky.social @iocbprague.bsky.social

Leaving Boston today after a great visit where we gave a hands-on training in #SQM affinity predictions. Now heading north to Maine, where I have the honor of chairing the GRS in #CADD & presenting our latest work at the #GRC.

Looking forward to the discussions, connections & science ahead!

🚨 Program Update: CADD GRS 2025!
We're excited to welcome @wpwalters.bsky.social as our keynote:
"AI in Drug Discovery – Revolution, Evolution, or Complete Nonsense?"
A perfect kickoff for an inspiring weekend in Portland!
🔗 www.grc.org/computer-aid...
#CADDGRS2025 #drugdesign #compchem

🏁 Program is live for the 2025 GRS on Computer-Aided Drug Design!

Overwhelming interest, top-tier abstracts, and a fantastic lineup incl. keynote Charlotte Deane + stellar mentorship panel. Can't wait!

🔗 www.grc.org/computer-aid...

#CADDGRS2025 #GRC #CompChem #DrugDesign

🚀 Exciting news! We're organizing a @cecamevents.bsky.social Flagship Workshop on Quantum Chemistry in Drug Design in Prague, Sept 8–10, 2025!

Join top experts from academia & industry. Few spots left for contributed talks!

📢 Apply now: www.cecam.org/workshop-det...

#compchem #cadd #QM #CECAM

Comparative Analysis of Quantum-Mechanical and standard Single-Structure Protein-Ligand Scoring Functions with MD-Based Free Energy Calculations Single-structure scoring functions have been considered inferior to expensive ensemble free energy methods in predicting protein-ligand affinities. We are revisiting this dogma with the recently devel...

Are single-structure scoring functions truly inferior to MD-based free energy methods? We recalibrated Wang dataset to test various approaches:
🔹 Conventional SFs (R² = 0.26)
🔹 SQM2.20 (R² = 0.47)
🔹 MD-based methods (R² = 0.52)
Check our newest preprint: doi.org/10.26434/che...
#cadd #compchem

(5/5) This work wouldn’t be possible without all incredible coauthors from indust&acad.

Thank you Christian Kramer, @jchodera.bsky.social , Kelly Damm-Ganamet, @bmix.bsky.social, Judith Günther, Uta Lessel, Richard Lewis, David Mobley, Eva Nittinger, @mattschap.bsky.social & @wpwalters.bsky.social!

(4/5) How do we push the field forward?

We need long-term, systematic benchmarking efforts with:

🔹 High-quality, unbiased datasets

🔹 Cross-industry collaboration

🔹 Open scientific discussions

Only then can we improve pose & activity prediction reliability in #SBDD!

#compchem #benchmarking

(3/5) Current pose- and activity- prediction benchmarks fall short.

Many datasets are biased, lack experimental validation, or fail to challenge methods properly. Blinded benchmarks ensure real-world performance, avoiding overfitting to known data.

#Benchmarking #compchem #cadd

(2/5) What makes an effective benchmark?

✅ Diverse datasets: drug-like molecules, hard targets, challenging interactions
✅ High-quality structures: clear density, reliable poses
✅ Robust affinity data: consistent Kd/Ki values
✅ Blinded validation: unbiased assessment

#compchem #benchmarking #cadd

🧵👇(1/5) Why does SBDD need better benchmarking?

Binding pose & activity predictions remain inconsistent, limiting drug discovery progress. A key issue? No standardized, widely accepted benchmark like CASP for protein structure prediction.

#Benchmarking #CADD #compchem

QM-based scoring function SQM2.20 - a universal yet computationally efficient physics-based method yielding reliable DFT quality affinity predictions in minutes!

www.nature.com/articles/s41...

+ new high-quality benchmark PL-REX dataset for the rigorous validation of your method

#compchem #cadd

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks Computational tools for structure-based drug design (SBDD) are widely used in drug discovery and can provide valuable insights to advance projects in an efficient and cost-effective manner. However, d...

New Perspective on Community Benchmarking in Structure-Based Drug Design (SBDD)!

#SBDD predictions need reliable benchmarks - diverse targets, high-quality affinity & structural data, and blinded validation. Let’s make it happen!

🔗 Read more: doi.org/10.1021/acs....

#DrugDiscovery #CompChem