Paulo Telles de Souza

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Publications

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Martini3-IDP: improved Martini 3 force field for disordered proteins

Liguo Wang , Christopher Brasnett , Luís Borges-Araújo , Paulo C T Souza , Siewert J Marrink
Nature Communications, 2025, 16 (1), pp.2874. ⟨10.1038/s41467-025-58199-2⟩
Article dans une revue hal-05377345 v1
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GōMartini 3: From large conformational changes in proteins to environmental bias corrections

Paulo C T Souza , Luís Borges-Araújo , Christopher Brasnett , Rodrigo A Moreira , Fabian Grünewald et al.
Nature Communications, 2025, 16 (1), pp.4051. ⟨10.1038/s41467-025-58719-0⟩
Article dans une revue hal-05377343 v1
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The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior

Kasper B Pedersen , Helgi I Ingólfsson , Daniel P Ramirez-Echemendia , Luís Borges-Araújo , Mikkel D Andreasen et al.
ACS Central Science, 2025, 11 (9), pp.1598−1610. ⟨10.1021/acscentsci.5c00755⟩
Article dans une revue hal-04880477 v2
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Martinize2 and Vermouth provide a unified framework for molecular topology generation

Peter C Kroon , Fabian Grünewald , Jonathan Barnoud , Marco van Tilburg , Chris Brasnett et al.
eLife, 2025, 12, ⟨10.7554/elife.90627⟩
Article dans une revue hal-05382479 v1
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Allosteric pathway connects Zn(II) loss from SOD1 to known pathogenic mechanisms

Rocío Araya-Osorio , Moisés Dominguez , Sebastian Thallmair , Siewert J Marrink , Paulo C T Souza et al.
International Journal of Biological Macromolecules, 2025, 331, pp.148349. ⟨10.1016/j.ijbiomac.2025.148349⟩
Article dans une revue hal-05377347 v1

The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior

Kasper Pedersen , Helgi Ingólfsson , Daniel Ramirez-Echemendia , Luís Borges-Araújo , Mikkel Andreasen et al.
ACS Central Science, 2025, 11 (9), pp.1598-1610. ⟨10.1021/acscentsci.5c00755⟩
Article dans une revue hal-05402465 v1

Martini 3 Coarse-Grained Models for Carbon Nanomaterials

Roshan Shrestha , Riccardo Alessandri , Martin Vögele , Cecile Hilpert , Paulo Souza et al.
Journal of Chemical Theory and Computation, 2025, 21 (18), pp.9035-9053. ⟨10.1021/acs.jctc.5c00923⟩
Article dans une revue hal-05402468 v1
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Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery

Markéta Paloncýová , Mariana Valério , Ricardo Nascimento dos Santos , Petra Kührová , Martin Šrejber et al.
Molecular Pharmaceutics, 2025, 22 (3), pp.1110-1141. ⟨10.1021/acs.molpharmaceut.4c00744⟩
Article dans une revue hal-05377340 v1
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Challenges in predicting PROTAC-mediated protein–protein interfaces with AlphaFold reveal a general limitation on small interfaces

Gilberto P Pereira , Corentin Gouzien , Paulo C T Souza , Juliette Martin
Bioinformatics Advances, 2025, 5 (1), ⟨10.1093/bioadv/vbaf056⟩
Article dans une revue hal-05400999 v1
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Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems

Mikkel D Andreasen , Paulo C T Souza , Birgit Schiøtt , Lorena Zuzic
Journal of Chemical Information and Modeling, 2025, 65 (10), pp.4760-4766. ⟨10.1021/acs.jcim.5c00069⟩
Article dans une revue hal-05377341 v1
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Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field

Astrid F Brandner , Iain P S Smith , Siewert J Marrink , Paulo C T Souza , Syma Khalid
Journal of Chemical Information and Modeling, 2025, ⟨10.1021/acs.jcim.4c01874⟩
Article dans une revue hal-04896377 v1
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Fast parameterization of Martini3 models for fragments and small molecules

Magdalena Szczuka , Gilberto P Pereira , Luis J Walter , Marc Gueroult , Pierre Poulain et al.
Journal of Chemical Theory and Computation, 2025, ⟨10.1101/2025.07.13.664596⟩
Article dans une revue hal-05377336 v1

Assessing the Martini 3 protein model: A review of its path and potential

Luís Borges-Araújo , Gilberto P Pereira , Mariana Valério , Paulo C. T. Souza
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2024, 1872 (4), pp.141014. ⟨10.1016/j.bbapap.2024.141014⟩
Article dans une revue hal-04745091 v1
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Martini 3 building blocks for Lipid Nanoparticle design

Lisbeth Ravnkilde Kjølbye , Mariana Valério , Markéta Paloncýová , Luís Borges-Araújo , Roberto Pestana-Nobles et al.
Journal of Chemical Theory and Computation, 2024, ⟨10.26434/chemrxiv-2024-bf4n8⟩
Article dans une revue hal-04745118 v1
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Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7

Simone Albani , Vishal Sudha Bhagavath Eswaran , Alessia Piergentili , Paulo C. T. Souza , Angelika Lampert et al.
International Journal of Biological Macromolecules, 2024, 278, pp.134219. ⟨10.1016/j.ijbiomac.2024.134219⟩
Article dans une revue hal-04745121 v1
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Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics

Gilberto P Pereira , Riccardo Alessandri , Moisés Domínguez , Rocío Araya-Osorio , Linus Grünewald et al.
Journal of Chemical Theory and Computation, 2024, 20 (13), pp.5763-5773. ⟨10.1021/acs.jctc.4c00275⟩
Article dans une revue hal-04745117 v1

Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex

Yeonji Chung , Chewon Yim , Gilberto Pereira , Sungjoon Son , Lisbeth Kjølbye et al.
Journal of Cell Biology, 2024, 223 (12), ⟨10.1083/jcb.202211035⟩
Article dans une revue hal-04896361 v1
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A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1

Alessio Bartocci , Andrea Grazzi , Nour Awad , Pierre-Jean Corringer , Paulo C. T. Souza et al.
Nature Communications, 2024, 15 (1), pp.9040. ⟨10.1038/s41467-024-53098-4⟩
Article dans une revue hal-04745126 v1
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OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field

Kasper B Pedersen , Luís Borges-Araújo , Amanda D Stange , Paulo C. T. Souza , Siewert-Jan Marrink et al.
Journal of Chemical Theory and Computation, 2024, ⟨10.1021/acs.jctc.4c00553⟩
Article dans une revue hal-04745097 v1
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Bending of a lipid membrane edge by annexin A5 trimers

Mayank Prakash Pandey , Paulo C. T. Souza , Weria Pezeshkian , Himanshu Khandelia
Biophysical Journal, 2024, 123 (8), pp.1006-1014. ⟨10.1016/j.bpj.2024.03.019⟩
Article dans une revue hal-04745112 v1
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Martini 3 coarse-grained models for carbon nanomaterials

Roshan Shrestha , Riccardo Alessandri , Martin Vögele , Cecile Hilpert , Paulo C T Souza et al.
Journal of Chemical Theory and Computation, 2024, 21 (18), pp.9035-9053. ⟨10.1021/acs.jctc.5c00923⟩
Article dans une revue hal-04882384 v1
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Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking

Gilberto P Pereira , Brian Jiménez-García , Riccardo Pellarin , Guillaume Launay , Sangwook Wu et al.
Journal of Chemical Information and Modeling, In press, ⟨10.1021/acs.jcim.3c01154⟩
Article dans une revue hal-04274715 v1

Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications

Panagiotis Koukos , Sepehr Dehghani-Ghahnaviyeh , Camilo Velez-Vega , John Manchester , D. Peter Tieleman et al.
Journal of Chemical Theory and Computation, 2023, 19 (23), pp.8901-8918. ⟨10.1021/acs.jctc.3c00604⟩
Article dans une revue hal-04745158 v1

Pragmatic Coarse-Graining of Proteins: Models and Applications

Luís Borges-Araújo , Ilias Patmanidis , Akhil Singh , Lucianna Santos , Adam Sieradzan et al.
Journal of Chemical Theory and Computation, 2023, 19 (20), pp.7112-7135. ⟨10.1021/acs.jctc.3c00733⟩
Article dans une revue (article de synthèse) hal-04296801 v1
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Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG

Charly Empereur-Mot , Kasper B Pedersen , Riccardo Capelli , Martina Crippa , Cristina Caruso et al.
Journal of Chemical Information and Modeling, 2023, 63 (12), pp.3827-3838. ⟨10.1021/acs.jcim.3c00530⟩
Article dans une revue hal-04296720 v1
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Expulsion mechanism of the substrate-translocating subunit in ECF transporters

Chancievan Thangaratnarajah , Mark Nijland , Luís Borges-Araújo , Aike Jeucken , Jan Rheinberger et al.
Nature Communications, 2023, 14 (1), pp.4484. ⟨10.1038/s41467-023-40266-1⟩
Article dans une revue hal-04296762 v1
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Identification of inhibitors targeting the energy-coupling factor (ECF) transporters

Eleonora Diamanti , Paulo Cesar Telles de Souza , Inda Setyawati , Spyridon Bousis , Leticia M Gómez et al.
Communications Biology, 2023, 6 (1), pp.1182. ⟨10.1038/s42003-023-05555-x⟩
Article dans une revue hal-04296925 v1
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Martini 3 Coarse-Grained Force Field for Cholesterol

Luís Borges-Araújo , Ana C Borges-Araújo , Tugba Nur Ozturk , Daniel P Ramirez-Echemendia , Balázs Fábián et al.
Journal of Chemical Theory and Computation, 2023, 19 (20), pp.7387-7404. ⟨10.1021/acs.jctc.3c00547⟩
Article dans une revue hal-04296756 v1

Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes

Neila Machado , Bart Bruininks , Priyanka Singh , Laurita dos Santos , Carine Dal Pizzol et al.
Nanoscale, 2022, 14 (2), pp.506-514. ⟨10.1039/D1NR04610A⟩
Article dans une revue hal-03863122 v1
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Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

Fabian Grünewald , Riccardo Alessandri , Peter C Kroon , Luca Monticelli , Paulo C T Souza et al.
Nature Communications, In press, 13 (1), pp.68. ⟨10.1038/s41467-021-27627-4⟩
Article dans une revue hal-03855658 v1
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Towards design of drugs and delivery systems with the Martini coarse-grained model

Lisbeth Kjølbye , Gilberto Pereira , Alessio Bartocci , Martina Pannuzzo , Simone Albani et al.
QRB Discovery, 2022, 3, pp.e19. ⟨10.1017/qrd.2022.16⟩
Article dans une revue hal-03864646 v1
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Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field

Luís Borges-Araújo , Paulo Souza , Fábio Fernandes , Manuel Melo
Journal of Chemical Theory and Computation, 2022, 18 (1), pp.357-373. ⟨10.1021/acs.jctc.1c00615⟩
Article dans une revue hal-03864628 v1
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Modelling structural properties of cyanine dye nanotubes at coarse-grained level

Ilias Patmanidis , Paulo Souza , Selim Sami , Remco Havenith , Alex de Vries et al.
Nanoscale Advances, 2022, 4 (14), pp.3033-3042. ⟨10.1039/D2NA00158F⟩
Article dans une revue hal-03864633 v1
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Two decades of Martini: Better beads, broader scope

Siewert Marrink , Luca Monticelli , Manuel Melo , Riccardo Alessandri , D. Peter Tieleman et al.
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2022, ⟨10.1002/wcms.1620⟩
Article dans une revue hal-03864638 v1
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Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

Bart Bruininks , Albert Thie , Paulo Souza , Tsjerk Wassenaar , Shirin Faraji et al.
Journal of Chemical Theory and Computation, 2021, 17 (12), pp.7873-7885. ⟨10.1021/acs.jctc.1c00446⟩
Article dans une revue hal-03863224 v1
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Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

Maria Tsanai , Pim W. Frederix , Carsten Schroer , Paulo Souza , Siewert Marrink
Chemical Science, 2021, 12 (24), pp.8521-8530. ⟨10.1039/D1SC00374G⟩
Article dans une revue hal-03863190 v1
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Martini 3: a general purpose force field for coarse-grained molecular dynamics

Paulo Souza , Riccardo Alessandri , Jonathan Barnoud , Sebastian Thallmair , Ignacio Faustino et al.
Nature Methods, 2021, 18 (4), pp.382-388. ⟨10.1038/s41592-021-01098-3⟩
Article dans une revue hal-03863208 v1
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Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties

Petteri Vainikka , Sebastian Thallmair , Paulo Cesar Telles Souza , Siewert Marrink
ACS Sustainable Chemistry & Engineering, In press, 9 (51), pp.17338-17350. ⟨10.1021/acssuschemeng.1c06521⟩
Article dans une revue hal-03864619 v1

Bottom-up fabrication of a proteasome–nanopore that unravels and processes single proteins

Shengli Zhang , Gang Huang , Roderick Corstiaan Abraham Versloot , Bart Marlon Herwig Bruininks , Paulo Cesar Telles de Souza et al.
Nature Chemistry, 2021, 13 (12), pp.1192-1199. ⟨10.1038/s41557-021-00824-w⟩
Article dans une revue hal-03863245 v1

Titratable Martini model for constant pH simulations

Fabian Grünewald , Paulo C. T. Souza , Haleh Abdizadeh , Jonathan Barnoud , Alex de Vries et al.
The Journal of Chemical Physics, 2020, 153 (2), ⟨10.1063/5.0014258⟩
Article dans une revue hal-04296865 v1
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Protein–ligand binding with the coarse-grained Martini model

Paulo C T Souza , Sebastian Thallmair , Paolo Conflitti , Carlos Ramírez-Palacios , Riccardo Alessandri et al.
Nature Communications, 2020, 11 (1), pp.3714. ⟨10.1038/s41467-020-17437-5⟩
Article dans une revue hal-04296809 v1
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Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction

Luis Itza Vazquez-Salazar , Michele Selle , Alex H de Vries , Siewert J Marrink , Paulo C T Souza
Green Chemistry, 2020, 22 (21), pp.7376-7386. ⟨10.1039/D0GC01823F⟩
Article dans une revue hal-04296861 v1

Toward a systematic modeling approach for coarse-grained carbohydrates

Astrid Brandner , Paulo C. T. Souza , Siewert Marrink , Syma Khalid
Biophysical Journal Supplement, Feb 2024, Philadelphia, United States. pp.297a, ⟨10.1016/j.bpj.2023.11.1849⟩
Communication dans un congrès hal-04745123 v1

A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations

Riccardo Alessandri , Sebastian Thallmair , Cristina Gil Herrero , Raúl Mera-Adasme , Siewert Marrink et al.
Yong Wang; Ruhong Zhou. A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, AIP Publishing LLCMelville, New York, pp.1-1-1-34, 2023, 978-0-7354-2524-8. ⟨10.1063/9780735425279_001⟩
Chapitre d'ouvrage hal-04305938 v1