DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences. - Jan Ludwiczak; Aleksander Winski; Krzysztof Szczepaniak; Vikram Alva; Stanislaw Dunin-Horkawicz (Bioinform., 2019)

Self-analysis of repeat proteins reveals evolutionarily conserved patterns. - Matthew Merski; Krzysztof Mlynarczyk; Jan Ludwiczak; Jakub Skrzeczkowski; Stanislaw Dunin-Horkawicz; Maria W. Górna (BMC Bioinform., 2020)

A library of coiled-coil domains: from regular bundles to peculiar twists. - Krzysztof Szczepaniak; Adriana Bukala; Antonio Marinho da Silva Neto; Jan Ludwiczak; Stanislaw Dunin-Horkawicz (Bioinform., 2021)

Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins. - Kamil Kaminski; Jan Ludwiczak; Maciej Jasinski; Adriana Bukala; Rafal Madaj; Krzysztof Szczepaniak; Stanislaw Dunin-Horkawicz (Briefings Bioinform., 2022)

localpdb - a Python package to manage protein structures and their annotations. - Jan Ludwiczak; Aleksander Winski; Stanislaw Dunin-Horkawicz (Bioinform., 2022)

AbDiffuser: full-atom generation of in-vitro functioning antibodies. - Karolis Martinkus; Jan Ludwiczak; Wei-Ching Liang; Julien Lafrance-Vanasse; Isidro Hötzel; Arvind Rajpal; Yan Wu 027; Kyunghyun Cho; Richard Bonneau; Vladimir Gligorijevic; Andreas Loukas (NeurIPS, 2023)

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models. - Kamil Kaminski; Jan Ludwiczak; Kamil Pawlicki; Vikram Alva; Stanislaw Dunin-Horkawicz (Bioinform., 2023)

Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins. - Frédéric A. Dreyer; Jan Ludwiczak; Karolis Martinkus; Brennan Abanades; Robert G. Alberstein; Pan Kessel; Pranav Rao; Jae Hyeon Lee; Richard Bonneau; Andrew M. Watkins; Franziska Seeger (CoRR, 2025)