Leandro Simonetti

Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases

Konstantinou, Aimiliani; Córdova-Pérez, Alicia; Varga, Julia K.; Madhu, Priyanka et al.

Part of Nature Communications, 2026

• DOI for Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
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A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3

Biswas, Soumi; Tavaf, Zohreh; Benz, Caroline; Khalil, Moustafa et al.

Part of Journal of Biological Chemistry, 2026

• DOI for A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
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Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets

Hamsikova, Marie; Hurdalek, Jan; Simonetti, Leandro; Ptacek, Jakub et al.

Part of Archives of Biochemistry and Biophysics, 2025

• DOI for Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets

Defining short linear motif binding determinants by phage display-based deep mutational scanning

Benz, Caroline; Maasen, Lars; Simonetti, Leandro; Mihalič, Filip et al.

Part of Protein Science, 2025

• DOI for Defining short linear motif binding determinants by phage display-based deep mutational scanning
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Trypanosoma brucei L19 is essential for ribosomal function

Zarate, Juan Manuel; Simonetti, Leandro; Manzur, Maria Jimena; Barroso, Juan Arturo Gomez et al.

Part of Biochemical and Biophysical Research Communications - BBRC, 2025

• DOI for Trypanosoma brucei L19 is essential for ribosomal function

Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases

Konstantinou, Aimiliani; Córdova-Pérez, Alicia; Varga, Julia K.; Madhu, Priyanka et al.

Part of Nature Communications, 2026

• DOI for Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases
• Download full text (pdf) of Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases

A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3

Biswas, Soumi; Tavaf, Zohreh; Benz, Caroline; Khalil, Moustafa et al.

Part of Journal of Biological Chemistry, 2026

• DOI for A tryptophan-phenylalanine binding motif for the histone methyltransferases MLL4 and MLL3
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Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets

Hamsikova, Marie; Hurdalek, Jan; Simonetti, Leandro; Ptacek, Jakub et al.

Part of Archives of Biochemistry and Biophysics, 2025

• DOI for Swapped domain orders in ZO-1 PDZ3 fusion proteins - implications for binding of established and novel targets

Defining short linear motif binding determinants by phage display-based deep mutational scanning

Benz, Caroline; Maasen, Lars; Simonetti, Leandro; Mihalič, Filip et al.

Part of Protein Science, 2025

• DOI for Defining short linear motif binding determinants by phage display-based deep mutational scanning
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Trypanosoma brucei L19 is essential for ribosomal function

Zarate, Juan Manuel; Simonetti, Leandro; Manzur, Maria Jimena; Barroso, Juan Arturo Gomez et al.

Part of Biochemical and Biophysical Research Communications - BBRC, 2025

• DOI for Trypanosoma brucei L19 is essential for ribosomal function

Elucidation of short linear motif‑based interactions of the MIT and rhodanese domains of the ubiquitin‑specific protease 8

Konstantinou, Aimiliani; Varga, Julia K.; Córdova-Pérez, Alicia; Simonetti, Leandro et al.

Part of Biology Direct, 2025

• DOI for Elucidation of short linear motif‑based interactions of the MIT and rhodanese domains of the ubiquitin‑specific protease 8
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Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD

Pagano, L.; Simonetti, Leandro; Pennacchietti, V.; Toto, A. et al.

Part of Biochemical and Biophysical Research Communications - BBRC, 2024

• DOI for Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD

Proteome-scale characterisation of motif-based interactome rewiring by disease mutations

Kliche, Johanna; Simonetti, Leandro; Krystkowiak, Izabella; Kuss, Hanna et al.

Part of Molecular Systems Biology, p. 1025-1048, 2024

• DOI for Proteome-scale characterisation of motif-based interactome rewiring by disease mutations
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ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers

Zhang, Yi; Xie, Guojia; Lee, Ji-Eun; Zandian, Mohamad et al.

Part of Nature Communications, 2024

• DOI for ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers
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Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Mihalič, Filip; Simonetti, Leandro; Giudice, Girolamo; Rubin Sander, Marie et al.

Part of Nature Communications, 2023

• DOI for Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
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The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome

Davey, Norman E.; Simonetti, Leandro; Ivarsson, Ylva

Part of Current opinion in structural biology, 2023

• DOI for The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome
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Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions

Kliche, Johanna; Garvanska, Dimitriya Hristoforova; Simonetti, Leandro; Badgujar, Dilip et al.

Part of Molecular Systems Biology, 2023

• DOI for Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions
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Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

Mihalic, Filip; Benz, Caroline; Kassa, Eszter; Lindqvist, Richard et al.

Part of Nature Communications, 2023

• DOI for Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
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Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions

Kassa, Eszter; Jamshidi, Sara; Mihalič, Filip; Simonetti, Leandro et al.

Part of Analytical Biochemistry, 2023

• DOI for Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions
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Presenting technological workflows

Sanchez, M. Florencia; Iselin, Louisa; Simonetti, Leandro

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 587-589, 2023

• DOI for Presenting technological workflows

ProP-PD for proteome-wide motif-mediated interaction discovery

Davey, Norman E.; Simonetti, Leandro; Ivarsson, Ylva

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 547-548, 2022

• DOI for ProP-PD for proteome-wide motif-mediated interaction discovery
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Proteome-scale mapping of binding sites in the unstructured regions of the human proteome

Benz, Caroline; Ali, Muhammad; Krystkowiak, Izabella; Simonetti, Leandro et al.

Part of Molecular Systems Biology, 2022

• DOI for Proteome-scale mapping of binding sites in the unstructured regions of the human proteome
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Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities

Kruse, Thomas; Benz, Caroline; Garvanska, Dimitriya H.; Lindqvist, Richard et al.

Part of Nature Communications, 2021

• DOI for Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities
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Recombinant antibody against Trypanosoma cruzi from patients with chronic Chagas heart disease recognizes mammalian nervous system

Niborski, Leticia L.; Potenza, Mariana; Chirivi, Renato G. S.; Simonetti, Leandro et al.

Part of EBioMedicine, 2021

• DOI for Recombinant antibody against Trypanosoma cruzi from patients with chronic Chagas heart disease recognizes mammalian nervous system
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Genetically Encoded Cyclic Peptide Phage Display Libraries

Simonetti, Leandro; Ivarsson, Ylva

Part of ACS CENTRAL SCIENCE, p. 336-338, 2020

• DOI for Genetically Encoded Cyclic Peptide Phage Display Libraries
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An update on genetic variants of the NKX2-5

Kolomenski, Jorge E.; Delea, Marisol; Simonetti, Leandro; Fabbro, Monica C. et al.

Part of Human Mutation, p. 1187-1208, 2020

• DOI for An update on genetic variants of the NKX2-5

SLiM-binding pockets: an attractive target for broad-spectrum antivirals

Simonetti, Leandro; Nilsson, Jakob; McInerney, Gerald; Ivarsson, Ylva et al.

Part of TIBS -Trends in Biochemical Sciences. Regular ed., p. 420-427, 2023

• DOI for SLiM-binding pockets: an attractive target for broad-spectrum antivirals
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Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions

Kassa, Eszter; Jamshidi, Sara; Mihalič, Filip; Simonetti, Leandro et al.

• DOI for Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions

Systematic discovery of short linear motif binding across human E3 ubiquitin ligases

Vieler, Maximilian; Varga, Julia K.; Gomez-Lucas, Lidia; Simonetti, Leandro et al.

Proteome-scale identification of short linear binding motifs for the BTB-KELCH E3 ligase family

Chen, Xiangrong; Vieler, Maximilian; Chen, Zhuoyao; Benz, Caroline et al.