Publications

List of publications by Stanisław Dunin-Horkawicz:

Madaj R, Martinez-Goikoetxea M, Kamiński K, Ludwiczak J, Dunin-Horkawicz S
Applicability of AlphaFold2 in the modeling of dimeric, trimeric, and tetrameric coiled-coil domains.
Protein Sci., 2025, Jan;34(1)
[PubMed]

Wiński A, Ludwiczak J, Orłowska M, Madaj R, Kamiński K, Dunin-Horkawicz S
AlphaFold2 captures the conformational landscape of the HAMP signaling domain.
Protein Sci., 2024, Jan;33(1)
[PubMed]

Kamiński K, Ludwiczak J, Pawlicki K, Alva V, Dunin-Horkawicz S
pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.
Bioinformatics., 2023, Oct 3;39(10)
[PubMed]

Ludwiczak J, Wiński A, Szczepaniak K, Alva V, Dunin-Horkawicz S
DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences.
Bioinformatics., 2019, Jan 2
[PubMed]

Ludwiczak J, Wiński A, Marinho A, Szczepaniak K, Alva V, Dunin-Horkawicz S
PiPred - a deep-learning method for prediction of π-helices in protein sequences.
Sci Rep., 2019, May 3;9(1):6888
[PubMed]

Nowacka M, Boccaletto P, Jankowska E, Jarzynka T, Bujnicki JM, Dunin-Horkawicz S
RRMdb-an evolutionary-oriented database of RNA recognition motif sequences.
Database (Oxford)., 2019, Jan 1
[PubMed]

Ludwiczak J, Jarmula A, Dunin-Horkawicz S
Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.
J Struct Biol., 2018, Jul;203(1):54-61
[PubMed]

Lupas AN, Bassler J, Dunin-Horkawicz S
The Structure and Topology of α-Helical Coiled Coils.
Subcell Biochem., 2017, 82:95-129
[PubMed]

Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S
Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts.
Genome Biol Evol., 2016, Jan 18;8(2):426-38
[PubMed]

Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FH
The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein.
J Mol Biol., 2015, Sep 25;427(19):3001-22
[PubMed]

Ferris HU, Zeth K, Hulko M, Dunin-Horkawicz S, Lupas AN
Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor.
J Struct Biol., 2014, Jun;186(3):349-56
[PubMed]

Dunin-Horkawicz S, Kopec KO, Lupas AN
Prokaryotic ancestry of eukaryotic protein networks mediating innate immunity and apoptosis.
J Mol Biol., 2014, Apr 3;426(7):1568-82
[PubMed]

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification.
Nucleic Acids Res., 2014, Apr;42(7):4160-79
[PubMed]

Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S
S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA.
RNA., 2013, Oct;19(10):1341-8
[PubMed]

Ferris HU, Dunin-Horkawicz S, Hornig N, Hulko M, Martin J, Schultz JE, Zeth K, Lupas AN, Coles M
Mechanism of regulation of receptor histidine kinases.
Structure., 2012, Jan 11;20(1):56-66
[PubMed]

Dunin-Horkawicz S, Lupas AN
Measuring the conformational space of square four-helical bundles with the program samCC.
J Struct Biol., 2010, May;170(2):226-35
[PubMed]

Dunin-Horkawicz S, Lupas AN
Comprehensive analysis of HAMP domains: implications for transmembrane signal transduction.
J Mol Biol., 2010, Apr 16;397(5):1156-74
[PubMed]

Dunin-Horkawicz S, Feder M, Bujnicki JM
Phylogenomic analysis of the GIY-YIG nuclease superfamily.
BMC Genomics., 2006, Apr 28;7:98
[PubMed]

Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM
MODOMICS: a database of RNA modification pathways.
Nucleic Acids Res., 2006, Jan 1;34(Database issue):D145-9
[PubMed]

Smug BJ, Szczepaniak K, Rocha EPC, Dunin-Horkawicz S, Mostowy RJ
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts.
Nat Commun., 2023, Nov 28;14(1)
[PubMed]

Ludwiczak J, Wiński A, Dunin-Horkawicz S
localpdb—a Python package to manage protein structures and their annotations.
Bioinformatics., 2022, Apr 28;38(9):2633–5
[PubMed]

Kamiński K, Ludwiczak J, Jasiński M, Bukala A, Madaj R, Szczepaniak K, Dunin-Horkawicz S
Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.
Brief Bioinform., 2022, Jan 17;23(1)
[PubMed]

Szczepaniak K, Bukala A, da Silva Neto AM, Ludwiczak J, Dunin-Horkawicz S
A library of coiled-coil domains: from regular bundles to peculiar twists.
Bioinformatics., 2021, Apr 1;36(22-23):5368-5376
[PubMed]

Merski M, Młynarczyk K, Ludwiczak J, Skrzeczkowski J, Dunin-Horkawicz S, Górna MW
Self-analysis of repeat proteins reveals evolutionarily conserved patterns.
BMC Bioinformatics., 2020, May 7;21(1):179
[PubMed]

Szczepaniak K, Ludwiczak J, Wiński A, Dunin-Horkawicz S
Variability of the core geometry in parallel coiled-coil bundles.
J Struct Biol., 2018, Oct;204(1):117-124
[PubMed]

Szczepaniak K, Lach G, Bujnicki JM, Dunin-Horkawicz S
Designability landscape reveals sequence features that define axial helix rotation in four-helical homo-oligomeric antiparallel coiled-coil structures.
J Struct Biol., 2014, Nov;188(2):123-33
[PubMed]

Tomecki R, Drazkowska K, Madaj R, Mamot A, Dunin-Horkawicz S, Sikorski PJ
Expanding the Available RNA Labeling Toolbox With CutA Nucleotidyltransferase for Efficient Transcript Labeling with Purine and Pyrimidine Nucleotide Analogs.
Chembiochem., 2024, Aug 1;25(15)
[PubMed]

Berdyński M, Ludwiczak J, Barczak A, Barcikowska-Kotowicz M, Kuźma-Kozakiewicz M, Dunin-Horkawicz S, et al.
TREM2 Gene Compound Heterozygosity in Neurodegenerative Disorders.
J Alzheimers Dis., 2022, 89(4):1211–9
[PubMed]

Latoszek E, Wiweger M, Ludwiczak J, Dunin-Horkawicz S, Kuznicki J, Czeredys M
Siah-1-interacting protein regulates mutated huntingtin protein aggregation in Huntington’s disease models.
Cell Biosci., 2022, Mar 19;12(1)
[PubMed]

Zayats V, Perlinska AP, Jarmolinska AI, Jastrzebski B, Dunin-Horkawicz S, Sulkowska JI
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor.
PLoS Comput Biol., 2021, Oct;17(10):e1009502
[PubMed]

Adamczyk M, Lewicka E, Szatkowska R, Nieznanska H, Ludwiczak J, Jasiński M, Dunin-Horkawicz S
Revealing biophysical properties of KfrA-type proteins as a novel class of cytoskeletal, coiled-coil plasmid-encoded proteins.
BMC Microbiol., 2021, Jan 22;21(1):32
[PubMed]

Banaś AM, Bocian-Ostrzycka KM, Dunin-Horkawicz S, Ludwiczak J, Wilk P, Orlikowska M, et al.
Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis.
Int J Mol Sci., 2021, Dec 15;22(24)
[PubMed]

Banaś AM, Bocian-Ostrzycka KM, Plichta M, Dunin-Horkawicz S, Ludwiczak J, Płaczkiewicz J, et al.
C8J_1298, a bifunctional thiol oxidoreductase of Campylobacter jejuni, affects Dsb (disulfide bond) network functioning.
PLoS One., 2020, 15(3):e0230366
[PubMed]

Jarmula A, Łusakowska A, Fichna JP, Topolewska M, Macias A, Johnson K, Töpf A, Straub V, Rosiak E, Szczepaniak K, Dunin-Horkawicz S, Maruszak A, Kaminska AM, Redowicz MJ
ANO5 mutations in the Polish limb girdle muscular dystrophy patients: Effects on the protein structure.
Sci Rep., 2019, Aug 8;9(1):11533
[PubMed]

Boccaletto P, Magnus M, Almeida C, Zyla A, Astha A, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki TK, Boniecki MJ, Stefaniak F, Bujnicki JM
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.
Nucleic Acids Res., 2018, Jan 4;46(D1):D202-D205
[PubMed]

Grzeszczuk MJ, Bąk A, Banaś AM, Urbanowicz P, Dunin-Horkawicz S, Gieldon A, Czaplewski C, Liwo A, Jagusztyn-Krynicka EK
Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase.
PLoS One., 2018, Apr 20;13(4):e0195358
[PubMed]

Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM
tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs.
Methods., 2016, Sep 1;107:34-41
[PubMed]

Machnicka MA, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.
BMC Bioinformatics., 2015, Oct 23;16:336
[PubMed]

Korycinski M, Albrecht R, Ursinus A, Hartmann MD, Coles M, Martin J, Dunin-Horkawicz S, Lupas AN
STAC--A New Domain Associated with Transmembrane Solute Transport and Two-Component Signal Transduction Systems.
J Mol Biol., 2015, Oct 9;427(20):3327-39
[PubMed]

Bocian-Ostrzycka KM, Łasica AM, Dunin-Horkawicz S, Grzeszczuk MJ, Drabik K, Dobosz AM, Godlewska R, Nowak E, Collet JF, Jagusztyn-Krynicka EK
Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain.
Front Microbiol., 2015, Oct 8;6:1065
[PubMed]

Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC
A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing.
Elife., 2015, Jul 10;4:e07320
[PubMed]

Grabowska AD, Wywiał E, Dunin-Horkawicz S, Łasica AM, Wösten MM, Nagy-Staroń A, Godlewska R, Bocian-Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki JM, van Putten JP, Jagusztyn-Krynicka EK
Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA.
PLoS One., 2014, Sep 2;9(9):e106247
[PubMed]

Hartmann MD, Dunin-Horkawicz S, Hulko M, Martin J, Coles M, Lupas AN
A soluble mutant of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity.
J Struct Biol., 2014, Jun;186(3):357-66
[PubMed]

Xu C, Liu R, Mehta AK, Guerrero-Ferreira RC, Wright ER, Dunin-Horkawicz S, Morris K, Serpell LC, Zuo X, Wall JS, Conticello VP
Rational design of helical nanotubes from self-assembly of coiled-coil lock washers.
J Am Chem Soc., 2013, Oct 16;135(41):15565-78
[PubMed]

Machnicka MA, Milanowska K, Osman Oglou O, Purta E, Kurkowska M, Olchowik A, Januszewski W, Kalinowski S, Dunin-Horkawicz S, Rother KM, Helm M, Bujnicki JM, Grosjean H
MODOMICS: a database of RNA modification pathways--2013 update.
Nucleic Acids Res., 2013, Jan;41(Database issue):D262-7
[PubMed]

Hartmann MD, Grin I, Dunin-Horkawicz S, Deiss S, Linke D, Lupas AN, Hernandez Alvarez B
Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria.
Proc Natl Acad Sci U S A., 2012, Dec 18;109(51):20907-12
[PubMed]

Poleszak K, Kaminska KH, Dunin-Horkawicz S, Lupas A, Skowronek KJ, Bujnicki JM
Delineation of structural domains and identification of functionally important residues in DNA repair enzyme exonuclease VII.
Nucleic Acids Res., 2012, Sep;40(16):8163-74
[PubMed]

Ferris HU, Dunin-Horkawicz S, Mondéjar LG, Hulko M, Hantke K, Martin J, Schultz JE, Zeth K, Lupas AN, Coles M
The mechanisms of HAMP-mediated signaling in transmembrane receptors.
Structure., 2011, Mar 9;19(3):378-85
[PubMed]

Alvarez BH, Gruber M, Ursinus A, Dunin-Horkawicz S, Lupas AN, Zeth K
A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins.
J Struct Biol., 2010, May;170(2):236-45
[PubMed]

Hartmann MD, Ridderbusch O, Zeth K, Albrecht R, Testa O, Woolfson DN, Sauer G, Dunin-Horkawicz S, Lupas AN, Alvarez BH
A coiled-coil motif that sequesters ions to the hydrophobic core.
Proc Natl Acad Sci U S A., 2009, Oct 6;106(40):16950-5
[PubMed]

Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K
MODOMICS: a database of RNA modification pathways. 2008 update.
Nucleic Acids Res., 2009, Jan;37(Database issue):D118-21
[PubMed]

Alva V, Dunin-Horkawicz S, Habeck M, Coles M, Lupas AN
The GD box: a widespread noncontiguous supersecondary structural element.
Protein Sci., 2009, Sep;18(9):1961-6
[PubMed]

Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.
BMC Bioinformatics., 2007, Mar 5;8:73
[PubMed]

Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase.
BMC Mol Biol., 2006, Jul 18;7:23
[PubMed]