Jan Ludwiczak

Beyond profiles: supervised repeat annotation using protein embeddings

TREAD improves repeat annotation by using protein embeddings instead of sequence profiles, outperforming HMMER in low-data and high-divergence scenarios.

Property Enhancer - a data efficient multi-objective approach for functional antibody optimization

Property Enhancer optimizes antibody properties using a data-efficient framework, achieving significant affinity gains in both in silico and in vitro tests.

Arc/Arg3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles

This study identifies Arc/Arg3.1 as a regulator of PABPN1 nuclear speckles through direct binding, impacting mRNA processing during neuronal activity.

Lab-in-the-loop therapeutic antibody design with deep learning

This paper introduces a machine learning framework for therapeutic antibody design that integrates computational methods with experimental validation, resulting in significantly improved binding affinity for multiple targets.

Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains

This paper evaluates AlphaFold2's ability to model coiled-coil domains, showing improved prediction of oligomeric states compared to previous methods.

AlphaFold2 captures the conformational landscape of the HAMP signaling domain

The paper uses AlphaFold2 to generate 5000 models of the HAMP domain, revealing its conformational variability and structural conservation across families.

pLM-BLAST - distant homology detection based on direct comparison of sequence representations from protein language models

pLM-BLAST detects distant homology by comparing sequence embeddings from ProtT5, achieving accuracy comparable to HHsearch while being faster and capable of local alignments.

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann-fold proteins

This paper develops deep learning models to predict and design cofactor specificity in Rossmann-fold proteins, achieving nearly perfect accuracy in benchmark tests.