Radoslav Krivak
@rdkbio
🧬 Structural Bioinformatics | 💊 AI/ML for Drug Discovery | Geometric DL 🔬 @IOCBPrague, prev. PhD @cusbg @matfyz
Tal vez te guste
How long does it take to predict ligand binding sites for all 220k proteins in the PDB? P2Rank 2.5 does it in 3 hours on a single CPU (16-core amd 5950x)—2x faster than the previous version 🚀. The SwissProt subset of AlphaFoldDB (540k proteins) takes even less: under 2 hours…
😂
Benchmarks of SynthonGPT from our CTO!
SynthonGPT delivers up to 3.1× more unique scaffolds than established tools while maintaining higher chemical diversity.
Cool idea
This is how CellARC looks: @arcprize style tasks, but generated using cellular automata (and with tunable complexity). Leaderboard: cellarc.mireklzicar.com
Very happy @roman_bushuiev and I joined the amazing team led by @HannesStaerk to work on BoltzGen, a generative model for binder design based on Boltz-2. Excited what it will enable!
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project has been collaborating with many leading biologists who tested BoltzGen at an unprecedented scale, showing success on many novel targets and pushing its limits! 🧵..
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🧵
My fellow biologists we must do everything in our power to prevent this scenario
great book
Blindsight by Peter Watts (2006) is my standout fiction book of the year, by far. Grand, challenging, scary, and super autistic.
🚀 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…
bsc.es
PhD student in computational biophysics and machine learning (R1, FPI)
Reference: 596_25_LS_ESB_R1 Job title: PhD student in computational biophysics and machine learning (R1, FPI)
After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @BSC_CNS. Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬 Thanks to all who have been part of this process! tinyurl.com/4r9vf4zx
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
Termal: a fast and interactive terminal-based viewer for multiple sequence alignments. #MultipleSequenceAlignments #TerminalViewer #interactiveViewer #Bioinformatics @BioinfoAdv academic.oup.com/bioinformatics…
No one trolls with street names quite like Prague.
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.
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… @madAniceP @Lepsik_science @RezacChem @IOCBPrague #JCIM Vol65 Issue15 #compchem
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 , @IOCBPrague , @IOCBTech & to all participants for the energy & insights! #compchem #SQM #sciencetwitter
MLSB is coming to Copenhagen, DK 🎉 Submission is under the same portal, just simply indicate your location preference(s).
You asked and we listened...@workshopmlsb is excited to be expanding to Copenhagen, DK at @EurIPSConf 🎉 Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your ranked location preference in the submission portal💫
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 #DrugDesign #CECAMinPrague @IOCBPrague
Before and after inventing modern algebraic geometry
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 @IOCBPrague @cecamEvents
Closing Day2 with exciting talks: @Lepsik_science 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! @cecamEvents @IOCBPrague @IOCBTech
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 @IOCBPrague, @IOCBTech & @cecamEvents for support! #compchem #DrugDesign #SQM
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