Jiřı́ Vondrášek

A tale of two states: AlphaFold binding pockets on the apo-holo continuum

The paper analyzes AlphaFold's predicted binding pockets to determine their similarity to apo or holo states, finding most are holo-like and showing how state affects docking success.

Identification of the trail-following pheromone receptor in termites

The paper identifies PsimOR14 as the trail-following pheromone receptor in termites by functionally characterizing it using single sensillum recording and molecular dynamics simulations.

Non-consensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning

The paper shows that GC content increases around transcription factor binding sites across cell lines and proposes that this reflects a scanning mechanism for DNA binding.

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication

EXTRA-seq quantifies enhancer-promoter communication in endogenous contexts, revealing the TATA-box's role in modulating expression and improving gene expression prediction when integrated with deep learning models.

The LOTUS Initiative for Open Natural Products Research: Knowledge Management through Wikidata

The paper introduces the LOTUS initiative, which curates and shares 750,000+ structure-organism pairs via Wikidata to improve data interoperability and knowledge management in natural products research.

Unevolved proteins from modern and prebiotic amino acids manifest distinct structural profiles

This study shows that proteins made from prebiotic and modern amino acids can form stable structures, challenging the idea that complex amino acids are necessary for protein folding.

GigaSOM.jl: High-perfomance clustering and visualization of huge cytometry datasets

GigaSOM.jl provides a scalable solution for clustering and visualizing large cytometry datasets, achieving high performance with distributed computing.

SOM-based embedding improves efficiency of high-dimensional cytometry data analysis

EmbedSOM improves high-dimensional cytometry data analysis by providing efficient, scalable visualization of cell populations and transitions without downsampling.