banner
adampecina.bsky.social
Adam Pecina
@adampecina.bsky.social
110 followers 150 following 24 posts
Computational Chemist | Researcher at IOCB Prague 🇨🇿 I specialize in quantum chemistry and computational drug design. Alumnus of Charles University & Palacký University. Former postdoc at the Italian Institute of Technology & Marie Curie (IF) Fellow.
Posts Media Videos Starter Packs
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 23d
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?
1
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 24d
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
1 7
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 24d
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
2
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 28d
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
2 6
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 29d
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
1 5
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 29d
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
2 6
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 29d
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
1 5
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · 29d
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
4 9
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Sep 8
You are greatly missed here Oles! Hope all went well on your side and meet you next time!
1 1
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Sep 8
www.linkedin.com/posts/adampe...
#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
1
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Sep 8
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
1 2 5
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Sep 7
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
3 9
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Jul 12
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!
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Jun 9
🚨 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
1
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · May 23
🏁 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
2025 Computer Aided Drug Design (GRS) Seminar GRC
The 2025 Gordon Research Seminar on Computer Aided Drug Design (GRS) will be held in Portland, Maine. Apply today to reserve your spot.
www.grc.org
5
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 24
🚀 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
CECAM - Quantum Chemistry for Drug Design: From Theory to Applications
www.cecam.org
6 12
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 17
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
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...
doi.org
1 7
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 12
(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!
2
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 12
(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
1 3
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 12
(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
1 2
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 12
(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 1
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 12
🧵👇(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
1 1
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 10
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
1 9
adampecina.bsky.social
Adam Pecina @adampecina.bsky.social · Mar 10
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
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...
doi.org
1 8 19