Ivan Koludarov

ProtSpace visualizes protein language model embeddings interactively, enabling hypothesis generation across biological scales without installation.

This study identifies three conserved genomic regions in ants as evolutionary hotspots for venom genes, revealing repeated recruitment to conserved platforms and diverse evolutionary dynamics.

The paper introduces a framework using MSA-Transformer to generate hybrid proteins between specified source and target proteins, producing sequences with higher consistency and plausibility than random baselines.

This study benchmarks fourteen protein-language models (pLMs) to determine which best captures biological properties, finding that mid-scale models often outperform larger ones for general tasks.

FlatProt provides 2D visualizations for comparing protein structures, enabling scalable and standardized analysis of large protein sets.

ProtSpace visualizes protein embeddings in 2D/3D to reveal functional patterns and challenges existing classifications in phage and venom protein analyses.

The paper reconstructs the evolutionary history of three-finger toxins (3FTxs) and identifies their non-toxin ancestor as a non-secretory Ly6 in squamate reptiles.

The paper reconstructs the evolutionary history of the g2 phospholipase A2 gene family across 93 vertebrate species to explore the origins of functional novelty.