| DeepCoil—a fast and accurate prediction of coiled-coil domains in protein sequences J Ludwiczak, A Winski, K Szczepaniak, V Alva, S Dunin-Horkawicz Bioinformatics 35 (16), 2790-2795, 2019 | 172 | 2019 |
| AbDiffuser: full-atom generation of in-vitro functioning antibodies K Martinkus, J Ludwiczak, WEIC LIANG, J Lafrance-Vanasse, I Hotzel, ... Advances in Neural Information Processing Systems 36, 2024 | 40 | 2024 |
| Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins K Kamiński, J Ludwiczak, M Jasiński, A Bukala, R Madaj, K Szczepaniak, ... Briefings in Bioinformatics 23 (1), bbab371, 2022 | 40 | 2022 |
| pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models K Kaminski, J Ludwiczak, K Pawlicki, V Alva, S Dunin-Horkawicz Bioinformatics 39 (10), btad579, 2023 | 33 | 2023 |
| A library of coiled-coil domains: from regular bundles to peculiar twists K Szczepaniak, A Bukala, AM da Silva Neto, J Ludwiczak, ... Bioinformatics 36 (22-23), 5368-5376, 2020 | 24 | 2020 |
| Combining Rosetta with molecular dynamics (MD): a benchmark of the MD-based ensemble protein design J Ludwiczak, A Jarmula, S Dunin-Horkawicz Journal of Structural Biology 203 (1), 54-61, 2018 | 24 | 2018 |
| PiPred–a deep-learning method for prediction of π-helices in protein sequences J Ludwiczak, A Winski, AM da Silva Neto, K Szczepaniak, V Alva, ... Scientific Reports 9 (1), 6888, 2019 | 17 | 2019 |
| Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N 4-hydroxy-dCMP J Ludwiczak, P Maj, P Wilk, T Frączyk, T Ruman, B Kierdaszuk, A Jarmuła, ... Molecular BioSystems 12 (4), 1333-1341, 2016 | 17 | 2016 |
| Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington’s disease models E Latoszek, M Wiweger, J Ludwiczak, S Dunin-Horkawicz, J Kuznicki, ... Cell & Bioscience 12 (1), 34, 2022 | 11 | 2022 |
| Self-analysis of repeat proteins reveals evolutionarily conserved patterns M Merski, K Młynarczyk, J Ludwiczak, J Skrzeczkowski, ... Bmc Bioinformatics 21, 1-17, 2020 | 8 | 2020 |
| β‐sheet breakers with consecutive phenylalanines: Insights into mechanism of dissolution of β‐amyloid fibrils A Jarmuła, J Ludwiczak, D Stępkowski Proteins: Structure, Function, and Bioinformatics 89 (7), 762-780, 2021 | 7 | 2021 |
| Interplay between DsbA1, DsbA2 and C8J_1298 periplasmic oxidoreductases of Campylobacter jejuni and their impact on bacterial physiology and pathogenesis AM Banaś, KM Bocian-Ostrzycka, S Dunin-Horkawicz, J Ludwiczak, ... International Journal of Molecular Sciences 22 (24), 13451, 2021 | 7 | 2021 |
| C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning AM Banaś, KM Bocian-Ostrzycka, M Plichta, S Dunin-Horkawicz, ... Plos one 15 (3), e0230366, 2020 | 7 | 2020 |
| localpdb—a Python package to manage protein structures and their annotations J Ludwiczak, A Winski, S Dunin-Horkawicz Bioinformatics 38 (9), 2633-2635, 2022 | 6 | 2022 |
| Variability of the core geometry in parallel coiled-coil bundles K Szczepaniak, J Ludwiczak, A Winski, S Dunin-Horkawicz Journal of Structural Biology 204 (1), 117-124, 2018 | 6 | 2018 |
| Crystal structures of nematode (parasitic T. spiralis and free living C. elegans), compared to mammalian, thymidylate synthases (TS). Molecular docking and molecular dynamics … A Jarmuła, P Wilk, P Maj, J Ludwiczak, A Dowierciał, K Banaszak, ... Journal of Molecular Graphics and Modelling 77, 33-50, 2017 | 6 | 2017 |
| AlphaFold2 captures the conformational landscape of the HAMP signaling domain A Winski, J Ludwiczak, M Orlowska, R Madaj, K Kaminski, ... Protein Science 33 (1), e4846, 2024 | 4 | 2024 |
| Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled‐coil domains R Madaj, M Martinez‐Goikoetxea, K Kaminski, J Ludwiczak, ... Protein Science 34 (1), e5244, 2025 | 2 | 2025 |
| Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins M Adamczyk, E Lewicka, R Szatkowska, H Nieznanska, J Ludwiczak, ... BMC microbiology 21, 1-16, 2021 | 2 | 2021 |
| TREM2 Gene Compound Heterozygosity in Neurodegenerative Disorders M Berdyński, J Ludwiczak, A Barczak, M Barcikowska-Kotowicz, ... Journal of Alzheimer's Disease 89 (4), 1211-1219, 2022 | 1 | 2022 |
