Paulo Telles de Souza

Publications

Article dans une revue (42)

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-05377345v1
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 Grünewaldet al. Nature Communications, 2025, 16 (1), pp.4051. ⟨10.1038/s41467-025-58719-0⟩ Article dans une revue hal-05377343v1
Martini 3 building blocks for Lipid Nanoparticle design Lisbeth Ravnkilde Kjølbye,Mariana Valério,Markéta Paloncýová,Luís Borges-Araújo,Roberto Pestana-Nobleset al. Journal of Chemical Theory and Computation, 2025, ⟨10.26434/chemrxiv-2024-bf4n8⟩ Article dans une revue hal-04745118v1
Martinize2 and Vermouth provide a unified framework for molecular topology generation Peter C Kroon,Fabian Grünewald,Jonathan Barnoud,Marco van Tilburg,Chris Brasnettet al. eLife, 2025, 12, ⟨10.7554/elife.90627⟩ Article dans une revue hal-05382479v1
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 Andreasenet al. ACS Central Science, 2025, 11 (9), pp.1598−1610. ⟨10.1021/acscentsci.5c00755⟩ Article dans une revue hal-04880477v2
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 Souzaet al. International Journal of Biological Macromolecules, 2025, 331, pp.148349. ⟨10.1016/j.ijbiomac.2025.148349⟩ Article dans une revue hal-05377347v1
The Martini 3 Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior Kasper Pedersen,Helgi Ingólfsson,Daniel Ramirez-Echemendia,Luís Borges-Araújo,Mikkel Andreasenet al. ACS Central Science, 2025, 11 (9), pp.1598-1610. ⟨10.1021/acscentsci.5c00755⟩ Article dans une revue hal-05402465v1
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery Markéta Paloncýová,Mariana Valério,Ricardo Nascimento dos Santos,Petra Kührová,Martin Šrejberet al. Molecular Pharmaceutics, 2025, 22 (3), pp.1110-1141. ⟨10.1021/acs.molpharmaceut.4c00744⟩ Article dans une revue hal-05377340v1
Martini 3 Coarse-Grained Models for Carbon Nanomaterials Roshan Shrestha,Riccardo Alessandri,Martin Vögele,Cecile Hilpert,Paulo Souzaet al. Journal of Chemical Theory and Computation, 2025, 21 (18), pp.9035-9053. ⟨10.1021/acs.jctc.5c00923⟩ Article dans une revue hal-05402468v1
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-05377341v1
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-05400999v1
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-04896377v1
Fast parameterization of Martini3 models for fragments and small molecules Magdalena Szczuka,Gilberto P Pereira,Luis J Walter,Marc Gueroult,Pierre Poulainet al. Journal of Chemical Theory and Computation, 2025, ⟨10.1101/2025.07.13.664596⟩ Article dans une revue hal-05377336v1
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-04745091v1
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 Lampertet al. International Journal of Biological Macromolecules, 2024, 278, pp.134219. ⟨10.1016/j.ijbiomac.2024.134219⟩ Article dans une revue hal-04745121v1
Bartender: Martini 3 Bonded Terms via Quantum Mechanics-Based Molecular Dynamics Gilberto P Pereira,Riccardo Alessandri,Moisés Domínguez,Rocío Araya-Osorio,Linus Grünewaldet al. Journal of Chemical Theory and Computation, 2024, 20 (13), pp.5763-5773. ⟨10.1021/acs.jctc.4c00275⟩ Article dans une revue hal-04745117v1
Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex Yeonji Chung,Chewon Yim,Gilberto Pereira,Sungjoon Son,Lisbeth Kjølbyeet al. Journal of Cell Biology, 2024, 223 (12), ⟨10.1083/jcb.202211035⟩ Article dans une revue hal-04896361v1
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 Marrinket al. Journal of Chemical Theory and Computation, 2024, ⟨10.1021/acs.jctc.4c00553⟩ Article dans une revue hal-04745097v1
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. Souzaet al. Nature Communications, 2024, 15 (1), pp.9040. ⟨10.1038/s41467-024-53098-4⟩ Article dans une revue hal-04745126v1
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-04745112v1
Martini 3 coarse-grained models for carbon nanomaterials Roshan Shrestha,Riccardo Alessandri,Martin Vögele,Cecile Hilpert,Paulo C T Souzaet al. Journal of Chemical Theory and Computation, 2024, 21 (18), pp.9035-9053. ⟨10.1021/acs.jctc.5c00923⟩ Article dans une revue hal-04882384v1
Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking Gilberto P Pereira,Brian Jiménez-García,Riccardo Pellarin,Guillaume Launay,Sangwook Wuet al. Journal of Chemical Information and Modeling, In press, ⟨10.1021/acs.jcim.3c01154⟩ Article dans une revue hal-04274715v1
Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications Panagiotis Koukos,Sepehr Dehghani-Ghahnaviyeh,Camilo Velez-Vega,John Manchester,D. Peter Tielemanet al. Journal of Chemical Theory and Computation, 2023, 19 (23), pp.8901-8918. ⟨10.1021/acs.jctc.3c00604⟩ Article dans une revue hal-04745158v1
Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG Charly Empereur-Mot,Kasper B Pedersen,Riccardo Capelli,Martina Crippa,Cristina Carusoet al. Journal of Chemical Information and Modeling, 2023, 63 (12), pp.3827-3838. ⟨10.1021/acs.jcim.3c00530⟩ Article dans une revue hal-04296720v1
Pragmatic Coarse-Graining of Proteins: Models and Applications Luís Borges-Araújo,Ilias Patmanidis,Akhil Singh,Lucianna Santos,Adam Sieradzanet 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-04296801v1
Expulsion mechanism of the substrate-translocating subunit in ECF transporters Chancievan Thangaratnarajah,Mark Nijland,Luís Borges-Araújo,Aike Jeucken,Jan Rheinbergeret al. Nature Communications, 2023, 14 (1), pp.4484. ⟨10.1038/s41467-023-40266-1⟩ Article dans une revue hal-04296762v1
Identification of inhibitors targeting the energy-coupling factor (ECF) transporters Eleonora Diamanti,Paulo Cesar Telles de Souza,Inda Setyawati,Spyridon Bousis,Leticia M Gómezet al. Communications Biology, 2023, 6 (1), pp.1182. ⟨10.1038/s42003-023-05555-x⟩ Article dans une revue hal-04296925v1
Martini 3 Coarse-Grained Force Field for Cholesterol Luís Borges-Araújo,Ana C Borges-Araújo,Tugba Nur Ozturk,Daniel P Ramirez-Echemendia,Balázs Fábiánet al. Journal of Chemical Theory and Computation, 2023, 19 (20), pp.7387-7404. ⟨10.1021/acs.jctc.3c00547⟩ Article dans une revue hal-04296756v1
Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes Neila Machado,Bart Bruininks,Priyanka Singh,Laurita dos Santos,Carine Dal Pizzolet al. Nanoscale, 2022, 14 (2), pp.506-514. ⟨10.1039/D1NR04610A⟩ Article dans une revue hal-03863122v1
Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials Fabian Grünewald,Riccardo Alessandri,Peter C Kroon,Luca Monticelli,Paulo C T Souzaet al. Nature Communications, In press, 13 (1), pp.68. ⟨10.1038/s41467-021-27627-4⟩ Article dans une revue hal-03855658v1
Towards design of drugs and delivery systems with the Martini coarse-grained model Lisbeth Kjølbye,Gilberto Pereira,Alessio Bartocci,Martina Pannuzzo,Simone Albaniet al. QRB Discovery, 2022, 3, pp.e19. ⟨10.1017/qrd.2022.16⟩ Article dans une revue hal-03864646v1
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-03864628v1
Modelling structural properties of cyanine dye nanotubes at coarse-grained level Ilias Patmanidis,Paulo Souza,Selim Sami,Remco Havenith,Alex de Vrieset al. Nanoscale Advances, 2022, 4 (14), pp.3033-3042. ⟨10.1039/D2NA00158F⟩ Article dans une revue hal-03864633v1
Two decades of Martini: Better beads, broader scope Siewert Marrink,Luca Monticelli,Manuel Melo,Riccardo Alessandri,D. Peter Tielemanet al. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2022, ⟨10.1002/wcms.1620⟩ Article dans une revue hal-03864638v1
Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies Bart Bruininks,Albert Thie,Paulo Souza,Tsjerk Wassenaar,Shirin Farajiet al. Journal of Chemical Theory and Computation, 2021, 17 (12), pp.7873-7885. ⟨10.1021/acs.jctc.1c00446⟩ Article dans une revue hal-03863224v1
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-03863190v1
Martini 3: a general purpose force field for coarse-grained molecular dynamics Paulo Souza,Riccardo Alessandri,Jonathan Barnoud,Sebastian Thallmair,Ignacio Faustinoet al. Nature Methods, 2021, 18 (4), pp.382-388. ⟨10.1038/s41592-021-01098-3⟩ Article dans une revue hal-03863208v1
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-03864619v1
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 Souzaet al. Nature Chemistry, 2021, 13 (12), pp.1192-1199. ⟨10.1038/s41557-021-00824-w⟩ Article dans une revue hal-03863245v1
Titratable Martini model for constant pH simulations Fabian Grünewald,Paulo C. T. Souza,Haleh Abdizadeh,Jonathan Barnoud,Alex de Vrieset al. The Journal of Chemical Physics, 2020, 153 (2), ⟨10.1063/5.0014258⟩ Article dans une revue hal-04296865v1
Protein–ligand binding with the coarse-grained Martini model Paulo C T Souza,Sebastian Thallmair,Paolo Conflitti,Carlos Ramírez-Palacios,Riccardo Alessandriet al. Nature Communications, 2020, 11 (1), pp.3714. ⟨10.1038/s41467-020-17437-5⟩ Article dans une revue hal-04296809v1
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-04296861v1

Pré-publication, Document de travail (6)

Martini 3 protein models - a practical introduction to different structure bias models and their comparison Thilo Duve,Liguo Wang,Luis Borges-Araujo,Siewert-Jan Marrink,Paulo C T Souzaet al. 2025 Pré-publication, Document de travail hal-05377333v1
A systematic approach to parameterization 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 2025 Pré-publication, Document de travail hal-04882146v1
GōMartini 3: From large conformational changes in proteins to environmental bias corrections Paulo C T Souza,Luís Borges-Araújo,Chris Brasnett,Rodrigo A Moreira,Fabian Grünewaldet al. 2024 Pré-publication, Document de travail hal-04745078v1
Challenges in predicting PROTAC-mediated Protein-Protein Interfaces with AlphaFold Gilberto P Pereira,Corentin Gouzien,Paulo Cesar Telles de Souza,Juliette Martin 2024 Pré-publication, Document de travail hal-04732948v1
Creating Coarse-Grained Systems with COBY: Towards Higher Accuracy in Membrane Complexity Mikkel D. M. D. Andreasen,Paulo C. T. Souza,Birgit Schiøtt,Lorena Zuzic 2024 Pré-publication, Document de travail hal-04745077v1
A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α 1 Alessio Bartocci,Paulo C.T. Souza,Marco Cecchini 2023 Pré-publication, Document de travail hal-04296779v1

Communication dans un congrès (1)

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-04745123v1

Chapitre d'ouvrage (1)

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 Marrinket 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-04305938v1