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Adam Pecina

@adampecina.bsky.social
129 followers 165 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.

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Adam Pecina @adampecina.bsky.social · 15/09/2025
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?
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Adam Pecina @adampecina.bsky.social · 15/09/2025
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
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Adam Pecina @adampecina.bsky.social · 15/09/2025
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
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Adam Pecina @adampecina.bsky.social · 10/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 09/09/2025
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
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Adam Pecina @adampecina.bsky.social · 08/09/2025
You are greatly missed here Oles! Hope all went well on your side and meet you next time!
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Adam Pecina @adampecina.bsky.social · 08/09/2025
www.linkedin.com/posts/adampe...
linkedin.com
#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...
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Adam Pecina @adampecina.bsky.social · 08/09/2025
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
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Adam Pecina @adampecina.bsky.social · 07/09/2025
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
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Adam Pecina @adampecina.bsky.social · 12/07/2025
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!
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Adam Pecina @adampecina.bsky.social · 09/06/2025
🚨 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
grc.org
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.
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Adam Pecina @adampecina.bsky.social · 23/05/2025
🏁 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
grc.org
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.
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Adam Pecina @adampecina.bsky.social · 24/03/2025
🚀 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.org
CECAM - Quantum Chemistry for Drug Design: From Theory to Applications
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Adam Pecina @adampecina.bsky.social · 17/03/2025
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
doi.org
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...
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Adam Pecina @adampecina.bsky.social · 12/03/2025
(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!
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Adam Pecina @adampecina.bsky.social · 12/03/2025
(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
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Adam Pecina @adampecina.bsky.social · 12/03/2025
(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
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Adam Pecina @adampecina.bsky.social · 12/03/2025
(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
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Adam Pecina @adampecina.bsky.social · 12/03/2025
🧵👇(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
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Adam Pecina @adampecina.bsky.social · 10/03/2025
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
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Adam Pecina @adampecina.bsky.social · 10/03/2025
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
doi.org
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...
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