AlphaPulldown2-a general pipeline for high-throughput structural modeling.

Molodenskiy D, Maurer VJ, Yu D, Chojnowski G, Bienert S, Tauriello G, Gilep K, Schwede T, Kosinski J

Bioinformatics (Oxford, England), 2025

doi:10.1093/bioinformatics/btaf115.

Nuclear pore permeability and fluid flow are modulated by its dilation state.

Hoffmann PC, Kim H, Obarska-Kosinska A, Kreysing JP, Andino-Frydman E, Cruz-León S, Margiotta E, Cernikova L, Kosinski J, Turoňová B, Hummer G, Beck M

Molecular cell, 2025

doi:10.1016/j.molcel.2024.11.038.

What shapes template-matching performance in cryogenic electron tomography in situ?

Maurer VJ, Siggel M, Kosinski J

Acta crystallographica. Section D, Structural biology, 2024

doi:10.1107/S2059798324004303.

ColabSeg: an interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data.

Siggel M, Jensen RK, Maurer VJ, Mahamid J, Kosinski J

Journal of structural biology, 2024

doi:10.1016/j.jsb.2024.108067.

PyTME (Python Template Matching Engine): a fast, flexible, and multi-purpose template matching library for cryogenic electron microscopy data.

Maurer VJ, Siggel M, Kosinski J

SoftwareX, 2024

doi:10.1016/j.softx.2024.101636.

RNA to rule them all: critical steps in Lassa virus ribonucleoparticle assembly and recruitment.

Sänger L, Williams HM, Yu D, Vogel D, Kosinski J, Rosenthal M, Uetrecht C

Journal of the American Chemical Society, 2023

doi:10.1021/jacs.3c07325.

Molecular basis of TASL recruitment by the peptide/histidine transporter 1, PHT1.

Custódio TF, Killer M, Yu D, Puente V, Teufel DP, Pautsch A, Schnapp G, Grundl M, Kosinski J, Löw C

Nature communications, 2023

doi:10.1038/s41467-023-41420-5.

Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles.

Sitarska E, Almeida SD, Beckwith MS, Stopp J, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt M, Kreshuk A, Erzberger A, Diz-Muñoz A

Nature communications, 2023

doi:10.1038/s41467-023-41173-1.

Structural and functional characterization of the Sin Nombre virus L protein.

Meier K, Thorkelsson SR, Durieux Trouilleton Q, Vogel D, Yu D, Kosinski J, Cusack S, Malet H, Grünewald K, Quemin ERJ, Rosenthal M

PLoS pathogens, 2023

doi:10.1371/journal.ppat.1011533.

A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation.

Wolf K, Kosinski J, Gibson TJ, Wesch N, Dötsch V, Genuardi M, Cordisco EL, Zeuzem S, Brieger A, Plotz G

Nucleic acids research, 2023

doi:10.1093/nar/gkad418.

Variable microtubule architecture in the malaria parasite.

Ferreira JL, Pražák V, Vasishtan D, Siggel M, Hentzschel F, Binder AM, Pietsch E, Kosinski J, Frischknecht F, Gilberger TW, Grünewald K

Nature communications, 2023

doi:10.1038/s41467-023-36627-5.

Integrative structural analysis of the type III secretion system needle complex from Shigella flexneri.

Flacht L, Lunelli M, Kaszuba K, Chen ZA, O' Reilly FJ, Rappsilber J, Kosinski J, Kolbe M

Protein science : a publication of the Protein Society, 2023

doi:10.1002/pro.4595.

The distance between the plasma membrane and the actomyosin cortex acts as a nanogate to control cell surface mechanics.

Lembo S, Strauss L, Cheng D, Vermeil J, Siggel M, Toro-Nahuelpan M, Chan CJ, Kosinski J, Piel M, Roure OD, Heuvingh J, Mahamid J, Diz-Muñoz A

bioRxiv, 2023

doi:10.1101/2023.01.31.526409.

Cryo-EM structure of the fully assembled Elongator complex.

Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NE, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S

Nucleic acids research, 2023

doi:10.1093/nar/gkac1232.

AlphaPulldown-a Python package for protein-protein interaction screens using AlphaFold-Multimer.

Yu D, Chojnowski G, Rosenthal M, Kosinski J

Bioinformatics , 2023

doi:10.1093/bioinformatics/btac749.

New opportunities in integrative structural modeling.

Ziemianowicz DS, Kosinski J

Current opinion in structural biology, 2022

doi:10.1016/j.sbi.2022.102488.

AI-based structure prediction empowers integrative structural analysis of human nuclear pores.

Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt FH, Margiotta E, Mackmull MT, Hagen WJH, Hummer G, Kosinski J, Beck M

Science (New York, N.Y.), 2022

doi:10.1126/science.abm9506.

Integrative structural modeling of macromolecular complexes using Assembline.

Rantos V, Karius K, Kosinski J

Nature protocols, 2021

doi:10.1038/s41596-021-00640-z.

Nuclear pores dilate and constrict in cellulo.

Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M

Science (New York, N.Y.), 2021

doi:10.1126/science.abd9776.

Integrative structural biology in the era of accurate structure prediction.

Masarati G, Landau M, Ben-Tal N, Lupas A, Kosloff M, Kosinski J

Journal of molecular biology, 2021

doi:10.1016/j.jmb.2021.167127.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M

Science advances, 2021

doi:10.1126/sciadv.abg9923.

Structure of the TFIIIC subcomplex τA provides insights into RNA polymerase III pre-initiation complex formation.

Vorländer MK, Jungblut A, Karius K, Baudin F, Grötsch H, Kosinski J, Müller CW

Nature communications, 2020

doi:10.1038/s41467-020-18707-y.

Structural role of essential light chains in the apicomplexan glideosome.

Pazicky S, Dhamotharan K, Kaszuba K, Mertens HDT, Gilberger T, Svergun D, Kosinski J, Weininger U, Löw C

Communications biology, 2020

doi:10.1038/s42003-020-01283-8.

In-cell architecture of the nuclear pore and snapshots of its turnover.

Allegretti M, Zimmerli CE, Rantos V, Wilfling F, Ronchi P, Fung HKH, Lee CW, Hagen W, Turoňová B, Karius K, Börmel M, Zhang X, Müller CW, Schwab Y, Mahamid J, Pfander B, Kosinski J, Beck M

Nature, 2020

doi:10.1038/s41586-020-2670-5.

Molecular basis of tRNA recognition by the Elongator complex.

Dauden MI, Jaciuk M, Weis F, Lin TY, Kleindienst C, Abbassi NEH, Khatter H, Krutyhołowa R, Breunig KD, Kosinski J, Müller CW, Glatt S

Science advances, 2019

doi:10.1126/sciadv.aaw2326.

Structure of prototypic peptide transporter DtpA from E. coli in complex with valganciclovir provides insights into drug binding of human PepT1.

Ural-Blimke Y, Flayhan A, Strauss J, Rantos V, Bartels K, Nielsen R, Pardon E, Steyaert J, Kosinski J, Quistgaard EM, Low C

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2019

doi:10.1021/jacs.8b11343.

From the resolution revolution to evolution: structural insights into the evolutionary relationships between vesicle coats and the nuclear pore.

Beck M, Mosalaganti S, Kosinski J

Current opinion in structural biology, 2018

doi:10.1016/j.sbi.2018.07.012.

In situ architecture of the algal nuclear pore complex.

Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M

Nature communications, 2018

doi:10.1038/s41467-018-04739-y.

Systematic analysis of protein turnover in primary cells.

Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM

Nature communications, 2018

doi:10.1038/s41467-018-03106-1.

A short linear motif in scaffold Nup145C connects Y-complex with pre-assembled outer ring Nup82 complex.

Teimer R, Kosinski J, von Appen A, Beck M, Hurt E

Nature communications, 2017

doi:10.1038/s41467-017-01160-9.

Structural insights into transcription initiation by yeast RNA polymerase I.

Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJ, Beck M, Sachse C, Müller CW

The EMBO journal, 2017

doi:10.15252/embj.201796958.

Architecture of the yeast Elongator complex

Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW

2016

doi:10.15252/embr.201643353.

Specialization versus Conservation: How Pol I and Pol III use the conserved architecture of the pre-initiation complex for specialized transcription.

Hoffmann NA, Sadian Y, Tafur L, Kosinski J, Müller CW

Transcription, 2016

doi:10.1080/21541264.2016.1203628.

Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle.

Bertipaglia C, Schneider S, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJ, Ravichandran AC, Wilmanns M, Kaksonen M, Briggs JA, Sachse C

EMBO reports, 2016

doi:10.15252/embr.201541960.

Automated structure modeling of large protein assemblies using crosslinks as distance restraints.

Ferber M, Kosinski J, Ori A, Rashid UJ, Moreno-Morcillo M, Simon B, Bouvier G, Batista PR, Müller CW, Beck M, Nilges M

Nature methods, 2016

doi:10.1038/nmeth.3838.

Molecular architecture of the inner ring scaffold of the human nuclear pore complex.

Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JA, Glavy JS, Hurt E, Beck M

Science (New York, N.Y.), 2016

doi:10.1126/science.aaf0643.

Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains.

Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S

Molecular cell, 2016

doi:10.1016/j.molcel.2015.11.016.

Molecular structures of unbound and transcribing RNA polymerase III.

Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJ, Sachse C, Müller CW

Nature, 2015

doi:10.1038/nature16143.

In situ structural analysis of the human nuclear pore complex.

von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P, Buczak K, Mosalaganti S, Hagen W, Andres-Pons A, Lemke EA, Bork P, Antonin W, Glavy JS, Bui KH, Beck M

Nature, 2015

doi:10.1038/nature15381.

Xlink Analyzer: Software for analysis and visualization of cross-linking data in the context of three-dimensional structures.

Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M

Journal of structural biology, 2015

doi:10.1016/j.jsb.2015.01.014.

REPAIRtoire - a database of DNA repair pathways

Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM

FEBS JOURNAL, 2013

doi:.

MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships

Kosinski J, Barbato A, Tramontano A

BIOINFORMATICS, 2013

doi:10.1093/bioinformatics/btt062.

Improving your target-template alignment with MODalign

Barbato A, Benkert P, Schwede T, Tramontano A, Kosinski J

BIOINFORMATICS, 2012

doi:10.1093/bioinformatics/bts070.

REPAIRtoire-a database of DNA repair pathways

Milanowska K, Krwawicz J, Papaj G, Kosinski J, Poleszak K, Lesiak J, Osinska E, Rother K, Bujnicki JM

NUCLEIC ACIDS RESEARCH, 2011

doi:10.1093/nar/gkq1087.

Identification of Lynch Syndrome Mutations in the MLH1-PMS2 Interface That Disturb Dimerization and Mismatch Repair

Kosinski J, Hinrichsen I, Bujnicki JM, Friedhoff P, Plotz G

HUMAN MUTATION, 2010

doi:10.1002/humu.21301.

Physiological truncation and domain organization of a novel uracil-DNA-degrading factor

Pukancsik M, Bekesi A, Klement E, Hunyadi-Gulyas E, Medzihradszky KF, Kosinski J, Bujnicki JM, Alfonso C, Rivas G, Vertessy BG

FEBS JOURNAL, 2010

doi:10.1111/j.1742-4658.2009.07556.x.

The PMS2 subunit of human MutL alpha contains a metal ion binding domain of the iron-dependent repressor protein family

Kosinski J, Plotz G, Guarne A, Bujnicki JM, Friedhoff P

JOURNAL OF MOLECULAR BIOLOGY, 2008

doi:10.1016/j.jmb.2008.06.056.

A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering

Kosinski J, Kubareva E, Bujnicki JM

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007

doi:10.1002/prot.21460.

Structure and Evolutionary Origin of Ca2+-Dependent Herring Type II Antifreeze Protein

Liu Y, Li ZJ, Lin QS, Kosinski J, Seetharaman J, Bujnicki JM, Sivaraman J, Hew CL

PLOS ONE, 2007

doi:10.1371/journal.pone.0000548.

Phylogenetic analysis of haloalkane dehalogenases

Chovancova E, Kosinski J, Bujnicki JM, Damborsky J

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007

doi:10.1002/prot.21313.

Novel protein fold discovered in the PabI family of restriction enzymes

Miyazono K, Watanabe M, Kosinski J, Ishikawa K, Kamo M, Sawasaki T, Nagata K, Bujnicki JM, Endo Y, Tanokura M, Kobayashi I

NUCLEIC ACIDS RESEARCH, 2007

doi:10.1093/nar/gkm091.

Theoretical model of restriction endonuclease HpaI in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis

Skowronek KJ, Kosinski J, Bujnicki JM

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2006

doi:10.1002/prot.20920.

Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry

Ahrends R, Kosinski J, Kirsch D, Manelyte L, Giron-Monzon L, Hummerich L, Schulz O, Spengler B, Friedhoff P

NUCLEIC ACIDS RESEARCH, 2006

doi:10.1093/nar/gkl407.

Crystal structure of Bacillus subtilis TrmB, the tRNA (m(7)G46) methyltransferase

Zegers I, Gigot D, van Vliet F, Tricot C, Aymerich S, Bujnicki JM, Kosinski J, Droogmans L

NUCLEIC ACIDS RESEARCH, 2006

doi:10.1093/nar/gkl116.

Analysis of the quaternary structure of the MutL C-terminal domain

Kosinski J, Steindorf I, Bujnicki JM, Giron-Monzon L, Friedhoff P

JOURNAL OF MOLECULAR BIOLOGY, 2005

doi:10.1016/j.jmb.2005.06.044.

The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function

Kosinski J, Feder M, Bujnicki JM

BMC BIOINFORMATICS, 2005

doi:10.1186/1471-2105-6-172.

Protein structure prediction by combination of fold-recognition with de novo folding

Bujnicki JM, Feder M, Gajda MJ, Kosinski J, Gront D, Kolinski A

FEBS JOURNAL, 2005

doi:.

FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6

Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005

doi:10.1002/prot.20726.

Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure

Ye XD, O'Neil PK, Foster AN, Gajda MJ, Kosinski J, Kurowski MA, Bujnicki JM, Friedman AM, Bailey-Kellogg C

PROTEIN SCIENCE, 2004

doi:10.1110/ps.04846604.