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Twinning for excellence in biophysics of protein interactions and self-assembly

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Data Management Plan (1)
Data management plan (opens in new window)
Websites, patent fillings, videos etc. (1)
Project website and digital platform structure (opens in new window)

Publications

Peer reviewed articles (44)
Constant-pH MD simulations of the protonation-triggered conformational switching in diphtheria toxin translocation domain (opens in new window)

Author(s): Nuno F.B. Oliveira, Alexey S. Ladokhin, Miguel Machuqueiro
Published in: Biophysical Journal, Issue 123, 2024, ISSN 0006-3495
Publisher: Elsevier BV
DOI: 10.1016/J.BPJ.2024.08.023

The Dimensionality of Hydrogen Bond Networks Induces Diverse Physical Properties of Peptide Crystals (opens in new window)

Author(s): Hui Yuan, Pierre-Andre Cazade, Chengqian Yuan, Bin Xue, Vijay Bhooshan Kumar, Rusen Yang, Gal Finkelstein-Zuta, Lihi Gershon, Maoz Lahav, Sigal Rencus-Lazar, Yi Cao, Davide Levy, Damien Thompson, Ehud Gazit
Published in: ACS Materials Letters, Issue 6, 2024, ISSN 2639-4979
Publisher: American Chemical Society (ACS)
DOI: 10.34961/RESEARCHREPOSITORY-UL.26561434

Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome (opens in new window)

Author(s): Pedro M. P. Fernandes; Romina A. Guedes; Bruno L. Victor; Jorge A. R. Salvador; Rita C. Guedes
Published in: Frontiers in Chemistry, Issue 11-2023, 2024, ISSN 2296-2646
Publisher: Frontiers Media
DOI: 10.3389/fchem.2023.1322628

Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease (opens in new window)

Author(s): Vasco Neto; Bruno Lourenço Victor; Nuno Galamba
Published in: Journal of Medicinal Chemistry, 2023, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.26434/chemrxiv-2023-qrzl0

S100B chaperone multimers suppress the formation of oligomers during Aβ42 aggregation (opens in new window)

Author(s): António J. Figueira; Joana Saavedra; Isabel Cardoso; Cláudio M. Gomes
Published in: Frontiers in Neuroscience, 2023, ISSN 1662-453X
Publisher: Frontiers
DOI: 10.3389/fnins.2023.1162741

Biophysical Studies of Amyloid-Binding Fluorophores to Tau AD Core Fibrils Formed without Cofactors (opens in new window)

Author(s): Daniela P. Freitas, Joana Saavedra, Isabel Cardoso, Cláudio M. Gomes
Published in: International Journal of Molecular Sciences, Issue 25, 2024, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/IJMS25189946

Recent advances on molecular dynamics-based techniques to address drug membrane permeability with atomistic detail (opens in new window)

Author(s): André M.M. Gomes, Paulo J. Costa, Miguel Machuqueiro
Published in: BBA Advances, Issue 4, 2023, ISSN 2667-1603
Publisher: Elsevier BV
DOI: 10.1016/J.BBADVA.2023.100099

A human microglial cell model of autosomal recessive spastic ataxia of Charlevoix-Saguenay (opens in new window)

Author(s): Fernanda Murtinheira, Elisa Farsetti, Luana Macedo, Ana Sofia Boasinha, Mario S. Rodrigues, Adelaide Fernandes, Federico Herrera
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Issue 1870, 2024, ISSN 0925-4439
Publisher: Elsevier BV
DOI: 10.1016/J.BBADIS.2024.167452

S100B chaperone multimers suppress the formation of oligomers during Aβ42 aggregation (opens in new window)

Author(s): António J. Figueira, Joana Saavedra, Isabel Cardoso, Cláudio M. Gomes
Published in: Frontiers in Neuroscience, Issue 17, 2023, ISSN 1662-453X
Publisher: Frontiers Media SA
DOI: 10.3389/FNINS.2023.1162741

Secondary Modification of S100B Influences Anti Amyloid-β Aggregation Activity and Alzheimer’s Disease Pathology (opens in new window)

Author(s): Romina Coelho; Chiara A. De Benedictis; Ann Katrin Sauer; António J. Figueira; Hélio Faustino; Andreas M. Grabrucker; Cláudio M. Gomes
Published in: International Journal of Molecular Sciences, 2024, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms25031787

Probing the Interactions of Thiazole Abietane Inhibitors with the Human Serine Hydrolases ABHD16A and ABHD12 (opens in new window)

Author(s): Tiina J. Ahonen, Choa P. Ng, Beatriz Farinha, Bárbara Almeida, Bruno L. Victor, Christopher Reynolds, Eija Kalso, Jari Yli-Kauhaluoma, Jennifer Greaves, Vânia M. Moreira
Published in: ACS Medicinal Chemistry Letters, Issue 14, 2023, ISSN 1948-5875
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACSMEDCHEMLETT.3C00313

Functional modulation of RAGE activation by multimeric S100B using single-domain antibodies (opens in new window)

Author(s): Margarida C. Simões, Joana S. Cristóvão, Els Pardon, Jan Steyaert, Günter Fritz, Cláudio M. Gomes
Published in: Journal of Biological Chemistry, Issue 300, 2024, ISSN 0021-9258
Publisher: Elsevier BV
DOI: 10.1016/J.JBC.2024.107983

Molecular Engineering of Ordered Piezoelectric Sulfonic Acid‐Containing Assemblies (opens in new window)

Author(s): Hui Yuan, Pierre‐Andre Cazade, Shuaikang Zhou, Linda J. W. Shimon, Chengqian Yuan, Dan Tan, Cunshun Liu, Wei Fan, Vijayakanth Thangavel, Yi Cao, Damien Thompson, Xuehai Yan, Rusen Yang, Bin Xue, Ehud Gazit
Published in: Small, Issue 20, 2023, ISSN 1613-6810
Publisher: Wiley
DOI: 10.1002/SMLL.202309493

Neuronal expression of S100B triggered by oligomeric Aβ peptide contributes to protection against cytoskeletal damage and synaptic loss (opens in new window)

Author(s): Joana Saavedra, Mariana Nascimento, António J. Figueira, Marina I. Oliveira da Silva, Tiago Gião, João Oliveira, Márcia A. Liz, Cláudio M. Gomes, Isabel Cardoso
Published in: Frontiers in Molecular Neuroscience, Issue 18, 2025, ISSN 1662-5099
Publisher: Frontiers Media SA
DOI: 10.3389/FNMOL.2025.1636365

Intrinsic bond strength index as a halogen bond interaction energy predictor (opens in new window)

Author(s): Ona Šivickytė, Paulo J. Costa
Published in: Physical Chemistry Chemical Physics, Issue 25, 2023, ISSN 1463-9076
Publisher: Royal Society of Chemistry (RSC)
DOI: 10.26434/CHEMRXIV-2022-C6NPJ-V3

Is There a Functional Role for the Knotted Topology in Protein UCH-L1? (opens in new window)

Author(s): Sara G. F. Ferreira, Manoj K. Sriramoju, Shang-Te Danny Hsu, Patrícia F. N. Faísca, Miguel Machuqueiro
Published in: Journal of Chemical Information and Modeling, Issue 64, 2024, ISSN 1549-9596
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.4C00880

A selection and optimization strategy for single-domain antibodies targeting the PHF6 linear peptide within the tau intrinsically disordered protein (opens in new window)

Author(s): Justine Mortelecque, Orgeta Zejneli, Séverine Bégard, Margarida C. Simões, Lea ElHajjar, Marine Nguyen, François-Xavier Cantrelle, Xavier Hanoulle, Jean-Christophe Rain, Morvane Colin, Cláudio M. Gomes, Luc Buée, Isabelle Landrieu, Clément Danis, Elian Dupré
Published in: Journal of Biological Chemistry, Issue 300, 2024, ISSN 0021-9258
Publisher: Elsevier BV
DOI: 10.1016/J.JBC.2024.107163EXTERNALLINK

Morphological and Biophysical Study of S100A9 Protein Fibrils by Atomic Force Microscopy Imaging and Nanomechanical Analysis (opens in new window)

Author(s): Ana P. Carapeto, Carlos Marcuello, Patrícia F. N. Faísca, Mário S. Rodrigues
Published in: Biomolecules, Issue 14, 2024, ISSN 2218-273X
Publisher: MDPI AG
DOI: 10.3390/BIOM14091091

Role of topology in protein thermal stability (opens in new window)

Author(s): João N. C. Especial, Beatriz P. Teixeira, Ana Nunes, Miguel Machuqueiro, Patrícia F. N. Faísca
Published in: Physical Review Research, Issue 8, 2026, ISSN 2643-1564
Publisher: American Physical Society (APS)
DOI: 10.1103/9KZY-W2TZ

Sacsin deletion decreases cell viscoelasticity and motility in a glial cell model of autosomal recessive spastic ataxia of Charlevoix Saguenay (opens in new window)

Author(s): Fernanda Murtinheira, João Belo, Ana Sofia Boasinha, Tiago T. Robalo, Vukosava M. Torres, Francisco R. Pinto, Constança Pimenta, Patricia Nascimento, Mario S. Rodrigues, Federico Herrera
Published in: Archives of Biochemistry and Biophysics, Issue 772, 2025, ISSN 0003-9861
Publisher: Elsevier BV
DOI: 10.1016/J.ABB.2025.110569

Unraveling the Aquaporin-3 Inhibitory Effect of Rottlerin by Experimental and Computational Approaches (opens in new window)

Author(s): Inês Paccetti-Alves; Marta S. P. Batista; Catarina Pimpão; Bruno L. Victor; Graça Soveral
Published in: International Journal of Molecular Sciences; Volume 24; Issue 6; Pages: 6004, 2023, ISSN 1422-0067
Publisher: MDPI
DOI: 10.3390/ijms24066004

Probing the Interactions of Thiazole Abietane Inhibitors with the Human Serine Hydrolases ABHD16A and ABHD12 (opens in new window)

Author(s): Tiina J. Ahonen; Choa P. N; Beatriz Farinha; Bárbara Almeida; Bruno L. Victor; Christopher Reynolds; Eija Kalso; Jari Yli-Kauhaluoma; Jennifer Greaves; Vânia M. Moreira
Published in: ACS Medicinal Chemistry Letters, 2023, ISSN 1948-5875
Publisher: American Chemical Society
DOI: 10.1021/acsmedchemlett.3c00313

Synthesis, Activity, Toxicity, and In Silico Studies of New Antimycobacterial N-Alkyl Nitrobenzamides (opens in new window)

Author(s): João P. Pais, Olha Antoniuk, David Pires, Tiago Delgado, Andreia Fortuna, Paulo J. Costa, Elsa Anes, Luis Constantino
Published in: Pharmaceuticals, Issue 17, 2024, ISSN 1424-8247
Publisher: MDPI AG
DOI: 10.3390/PH17050608

Conformation-Driven Phase Separation in the Linker Domain of Focal Adhesion Kinases (opens in new window)

Author(s): Lucy Martin, Daniela P. Freitas, Emmanuelle Boll, Alain Brans, Justine Mortelecque, François-Xavier Cantrelle, Pierre Dourlen, Cláudio M. Gomes, Clément Danis, Isabelle Landrieu
Published in: Biochemistry, Issue 64, 2025, ISSN 0006-2960
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACS.BIOCHEM.4C00677

Asymmetric post-translational modifications regulate the nuclear translocation of STAT3 homodimers in response to leukemia inhibitory factor (opens in new window)

Author(s): Mickael Diallo; Constança Pimenta; Fernanda Murtinheira; Daniela Martins-Alves; Francisco R. Pinto; André Abrantes da Costa; Ricardo Letra-Vilela; Vanesa Martin; Carmen Rodriguez; Mário S. Rodrigues; Federico Herrera
Published in: Cellular Oncology, 2023, ISSN 2211-3436
Publisher: Springer Nature
DOI: 10.21203/rs.3.rs-3188959/v1

Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations (opens in new window)

Author(s): Andreia Fortuna; Paulo J. Costa
Published in: Journal of Chemical Information and Modeling, 2023, ISSN 1549-9596
Publisher: ACS Publications
DOI: 10.26434/chemrxiv-2023-sgbfb

Cyclic Peptides as Aggregation Inhibitors for Sickle Cell Disease (opens in new window)

Author(s): Vasco Neto, Bruno Lourenço Victor, Nuno Galamba
Published in: Journal of Medicinal Chemistry, Issue 66, 2023, ISSN 0022-2623
Publisher: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2023-QRZL0

Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations (opens in new window)

Author(s): Andreia Fortuna, Paulo J. Costa
Published in: Journal of Chemical Information and Modeling, Issue 63, 2023, ISSN 1549-9596
Publisher: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2023-SGBFB

Amyloid-like Structures in Marine Adhesive Proteins (opens in new window)

Author(s): Mariana Rodrigues Santos, Bárbara Joana Henriques, Romana Santos
Published in: Marine Drugs, Issue 23, 2025, ISSN 1660-3397
Publisher: MDPI AG
DOI: 10.3390/MD23090363

Secondary Modification of S100B Influences Anti Amyloid-β Aggregation Activity and Alzheimer’s Disease Pathology (opens in new window)

Author(s): Romina Coelho, Chiara A. De Benedictis, Ann Katrin Sauer, António J. Figueira, Hélio Faustino, Andreas M. Grabrucker, Cláudio M. Gomes
Published in: International Journal of Molecular Sciences, Issue 25, 2024, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/IJMS25031787

Is spastic ataxia 8 a protein misfolding disorder? (opens in new window)

Author(s): Pedro Ferreira-Peralta; Brenda França; Fernanda Murtinheira; Mario S. Rodrigues; Federico Herrera
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 2023, ISSN 0925-4439
Publisher: Elsevier B.V.
DOI: 10.1016/j.bbadis.2023.166882

Recent advances on molecular dynamics-based techniques to address drug membrane permeability with atomistic detail (opens in new window)

Author(s): André M.M. Gomes; Paulo J. Costa; Miguel Machuqueiro
Published in: BBA Advances, 2023, ISSN 2667-1603
Publisher: Elsevier B.V.
DOI: 10.1016/j.bbadva.2023.100099

Influence of Iodine Merz–Singh–Kollman Radius on the Calculated Charges and Hydration Free Energies of Iodinated Molecules (opens in new window)

Author(s): Andreia Fortuna; Pedro M. S. Suzano; Miguel Machuqueiro; Paulo J. Costa
Published in: Journal of Computational Biophysics and Chemistry, Issue 04, 2024, ISSN 2737-4165
Publisher: World Scientific Publishing
DOI: 10.1142/S2737416523500722

Journal of Biological Chemistry (opens in new window)

Author(s): Justine Mortelecque; Orgeta Zejneli; Séverine Bégard; Margarida C. Simões; Lea ElHajjar; Marine Nguyen; François-Xavier Cantrelle; Xavier Hanoulle; Jean-Christophe Rain; Morvane Colin; Cláudio M. Gomes; Luc Buée; Isabelle Landrieu; ClémenDanis C, Dupré E.
Published in: Journal of Biological Chemistry, Issue 4, 2024, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2024.107163

S100B Mitigates Cytoskeletal and Mitochondrial Alterations in a Glial Cell Model of Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay (opens in new window)

Author(s): Ana Sofia Boasinha, Fernanda Murtinheira, Susana Solá, Cláudio M. Gomes, Federico Herrera
Published in: Molecular Neurobiology, Issue 62, 2025, ISSN 0893-7648
Publisher: Springer Science and Business Media LLC
DOI: 10.1007/S12035-025-05057-3

Cross-Interactions of Aβ Peptides Implicated in Alzheimer’s Disease Shape Amyloid Oligomer Structures and Aggregation (opens in new window)

Author(s): Tanja Habeck, Silvana Smilla Zurmühl, António J. Figueira, Edvaldo Vasconcelos Soares Maciel, Cláudio M. Gomes, Frederik Lermyte
Published in: ACS Chemical Neuroscience, Issue 15, 2024, ISSN 1948-7193
Publisher: American Chemical Society (ACS)
DOI: 10.1021/ACSCHEMNEURO.4C00492

Intrinsic Bond Strength Index as a halogen bond interaction energy predictor (opens in new window)

Author(s): Ona Šivickytė; Paulo J. Costa
Published in: Physical Chemistry Chemical Physics, 2023, ISSN 1463-9084
Publisher: Royal Society of Chemistry
DOI: 10.26434/chemrxiv-2022-c6npj

Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method (opens in new window)

Author(s): João G. N. Sequeira, Adrian E. Roitberg, Miguel Machuqueiro
Published in: Journal of Chemical Theory and Computation, Issue 21, 2025, ISSN 1549-9618
Publisher: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2025-38NFP

Folding and knotting of biotic and prebiotic amino acid sequences through reverse evolution (opens in new window)

Author(s): João N.C. Especial, Patrícia F.N. Faísca
Published in: Biophysical Journal, Issue 124, 2025, ISSN 0006-3495
Publisher: Elsevier BV
DOI: 10.1101/2025.06.04.657801

Discrete Actuation of Water‐Responsive Crystalline Metal–Peptide Frameworks (opens in new window)

Author(s): Hui Yuan, Yiming Tang, Elma Naranjo, Pierre‐Andre Cazade, Yifei Yao, Vijayakanth Thangavel, Rusen Yang, Sigal Rencus‐Lazar, Damien Thompson, Linda J. W. Shimon, Guanghong Wei, Xi Chen, Ehud Gazit
Published in: Angewandte Chemie International Edition, Issue 64, 2025, ISSN 1433-7851
Publisher: Wiley
DOI: 10.1002/ANIE.202513629

Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome (opens in new window)

Author(s): Pedro M. P. Fernandes, Romina A. Guedes, Bruno L. Victor, Jorge A. R. Salvador, Rita C. Guedes
Published in: Frontiers in Chemistry, Issue 11, 2024, ISSN 2296-2646
Publisher: Frontiers Media SA
DOI: 10.3389/FCHEM.2023.1322628

Is spastic ataxia 8 a protein misfolding disorder? (opens in new window)

Author(s): Pedro Ferreira-Peralta, Brenda França, Fernanda Murtinheira, Mario S. Rodrigues, Federico Herrera
Published in: Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Issue 1870, 2024, ISSN 0925-4439
Publisher: Elsevier BV
DOI: 10.1016/J.BBADIS.2023.166882

Asymmetric post-translational modifications regulate the nuclear translocation of STAT3 homodimers in response to leukemia inhibitory factor (opens in new window)

Author(s): Mickael Diallo, Constança Pimenta, Fernanda Murtinheira, Daniela Martins-Alves, Francisco R. Pinto, André Abrantes da Costa, Ricardo Letra-Vilela, Vanesa Martin, Carmen Rodriguez, Mário S. Rodrigues, Federico Herrera
Published in: Cellular Oncology, Issue 47, 2023, ISSN 2211-3428
Publisher: Springer Science and Business Media LLC
DOI: 10.21203/RS.3.RS-3188959/V1

Unraveling the Aquaporin-3 Inhibitory Effect of Rottlerin by Experimental and Computational Approaches (opens in new window)

Author(s): Inês Paccetti-Alves, Marta S. P. Batista, Catarina Pimpão, Bruno L. Victor, Graça Soveral
Published in: International Journal of Molecular Sciences, Issue 24, 2023, ISSN 1422-0067
Publisher: MDPI AG
DOI: 10.3390/IJMS24066004

Other (7)
Identifying functional sites at scale (opens in new window)

Author(s): Cagiada, Matteo
Published in: 2023
DOI: 10.5281/zenodo.10409579

Proximity Labelling Assays to Detect Protein Interactions in Cells (opens in new window)

Author(s): Bar, Daniel
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.14046998

Shifting KRAS hotspot mutations inhibition paradigm in colorectal cancer (opens in new window)

Author(s): Ana Rita Brás; Ana Lopes; Nuno Mendes; Paulo J. Costa; Anabela Ferreira; Sara Granja; Ana Paula Silva; Francisco Tortosa; Fátima Baltazar; Fátima Gärtner; Maria João Sousa; Andreia Valente; Ana Preto
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.08.09.552513

Computational tools to analyse protein stability and abundance (opens in new window)

Author(s): Schulze, Thea Klarsø
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.10783195

Understanding intrinsically disordered proteins: from integrative modelling to design (opens in new window)

Author(s): Pesce, Francesco
Published in: 2023
DOI: 10.5281/zenodo.10379566

Computational tools to analyse protein variant effects (opens in new window)

Author(s): Jonsson, Nicolas
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.10783189

Advanced Microscopy and Live Cell Imaging (opens in new window)

Author(s): Lisby, Michael
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.14046016

Thesis and dissertations (3)
Investigation of S100 proteins and their role in huntingtin aggregation

Author(s): Marta Sofia Silva da Cruz Botelho
Published in: ULisboa Repository, 2023
Publisher: Author Edition

The role of post-translational modifications on NKX6-2 behavior and function

Author(s): Brenda Gabriella França
Published in: NOVA University Repository, 2023
Publisher: Author Edition

Sea urchin inspired adhesive proteins - expression and purification of Nectin structural domains

Author(s): Mariana Rodrigues dos Santos
Published in: ULisboa Repository, 2023
Publisher: Author Edition

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Last update: 26 November 2025

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