Ivan Koludarov

ProtSpace: Protein Universe in Your Browser

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

How Ant Genomes Repeatedly Reinvent Venom

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.

Generating Hybrid Proteins with the MSA-Transformer

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.

Which pLM to choose?

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: 2D visualization eases protein structure comparison

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

ProtSpace: a tool for visualizing protein space

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

Domain loss enabled evolution of novel functions in a gene superfamily

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.

Reconstructing the evolutionary history of a functionally diverse gene2 family reveals complexity at the genetic origins of novelty

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