#research #compchem #drugdesign Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein–Ligand Scoring Functions with MD-Based Free Energy Calculations (Jalaie, Fanfrlík, Adam Pecina , Lepšík, Řezáč) – J. Chem. Inf. Model. ACS Publications:

Exciting to see our protein binder design pipeline BindCraft published in its final form in nature ! This has been an amazing collaborative effort with Lennart, Christian Schellhaas, Sergey Ovchinnikov, Bruno Correia and many other amazing lab members and collaborators. nature.com/articles/s4158…

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 #cadd #compchem #SQM IOCB Tech CECAM IOCB Prague

Day 1 of our #CECAM Flagship Workshop in Prague started strong! Talks by Kennie Merz, Jan Řezáč, Markus Rainer Hermann & Hamza Ibrahim sparked great discussion on #QM, #ML & #DrugDesign. Thanks to IOCB Prague, IOCB Tech & CECAM for support! #compchem #DrugDesign #SQM

Closing Day2 with exciting talks: Martin Lepsik on #SQM scoring on AI-generated structures, Matthias Hennemann on local properties at P-L interfaces & Igor Gordiy on enhanced sampling with ML potentials. Inspiring end before our social dinner! CECAM IOCB Prague IOCB Tech

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. #CECAMinPrague IOCB Prague CECAM

Before and after inventing modern algebraic geometry

Comparative Analysis of Quantum-Mechanical and Standard Single-Structure Protein–Ligand Scoring Functions with MD-Based Free Energy Calculations pubs.acs.org/doi/10.1021/ac… Adam Pecina Martin Lepsik Jan Řezáč IOCB Prague #JCIM Vol65 Issue15 #compchem

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! CECAM #DrugDesign #CECAMinPrague IOCB Prague

MLSB is coming to Copenhagen, DK 🎉 Submission is under the same portal, just simply indicate your location preference(s).

Our #CECAM Flagship Workshop brought together leading minds from academia & industry to push the boundaries of #QM, #ML & #MD in #DrugDesign. Big thanks to CECAM , IOCB Prague , IOCB Tech & to all participants for the energy & insights! #compchem #SQM #sciencetwitter

Guilty of this one myself. AI-drawn molecules look slick, but they’re chemically broken: fake bonds, VSEPR violations, bogus periodic tables. Until the models are ready, I'm in. Integrity > aesthetics.

No one trolls with street names quite like Prague.

Termal: a fast and interactive terminal-based viewer for multiple sequence alignments. #MultipleSequenceAlignments #TerminalViewer #interactiveViewer #Bioinformatics Bioinformatics Advances academic.oup.com/bioinformatics…

ngl i dont think you get to claim that alphafold2 weird architectural decisions were unnecessary if you are basically doing model distillation using the results of alphafold2 its a great title though...so i get it...sometimes aura takes precedence

🚀 As first official act, we are hiring! 🎓 We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded! More information here: bsc.es/join-us/job-op…

great book

My fellow biologists we must do everything in our power to prevent this scenario

We train machine learning models on millions of proteins. But when making predictions, do we need them to understand all proteins at once? Often we need an accurate model for the specific protein we are studying/designing. We address this with ProteinTTT arxiv.org/abs/2411.0210🧵

Very happy Roman Bushuiev and I joined the amazing team led by Hannes Stärk to work on BoltzGen, a generative model for binder design based on Boltz-2. Excited what it will enable!