Paulo Telles de Souza

Documents

Publications

	Martini 3 Coarse-Grained Force Field for Cholesterol Luís Borges-Araújo , Ana C Borges-Araújo , Tugba Nur Ozturk , Daniel P Ramirez-Echemendia , Balázs Fábián Journal of Chemical Theory and Computation, 2023, 19 (20), pp.7387-7404. ⟨10.1021/acs.jctc.3c00547⟩ Article dans une revue hal-04296756v1
	Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG Charly Empereur-Mot , Kasper B Pedersen , Riccardo Capelli , Martina Crippa , Cristina Caruso 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 Sieradzan Journal of Chemical Theory and Computation, 2023, 19 (20), pp.7112-7135. ⟨10.1021/acs.jctc.3c00733⟩ Article dans une revue hal-04296801v1
	Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking Gilberto P Pereira , Brian Jiménez-García , Riccardo Pellarin , Guillaume Launay , Sangwook Wu Journal of Chemical Information and Modeling, In press, ⟨10.1021/acs.jcim.3c01154⟩ Article dans une revue hal-04274715v1
	Identification of inhibitors targeting the energy-coupling factor (ECF) transporters Eleonora Diamanti , Paulo Cesar Telles de Souza , Inda Setyawati , Spyridon Bousis , Leticia M Gómez Communications Biology, 2023, 6 (1), pp.1182. ⟨10.1038/s42003-023-05555-x⟩ Article dans une revue hal-04296925v1
	Expulsion mechanism of the substrate-translocating subunit in ECF transporters Chancievan Thangaratnarajah , Mark Nijland , Luís Borges-Araújo , Aike Jeucken , Jan Rheinberger Nature Communications, 2023, 14 (1), pp.4484. ⟨10.1038/s41467-023-40266-1⟩ Article dans une revue hal-04296762v1
	Two decades of Martini: Better beads, broader scope Siewert Marrink , Luca Monticelli , Manuel Melo , Riccardo Alessandri , D. Peter Tieleman WIREs Computational Molecular Science, 2022, ⟨10.1002/wcms.1620⟩ Article dans une revue hal-03864638v1
	Modelling structural properties of cyanine dye nanotubes at coarse-grained level Ilias Patmanidis , Paulo Souza , Selim Sami , Remco Havenith , Alex de Vries Nanoscale Advances, 2022, 4 (14), pp.3033-3042. ⟨10.1039/D2NA00158F⟩ Article dans une revue hal-03864633v1
	Towards design of drugs and delivery systems with the Martini coarse-grained model Lisbeth Kjølbye , Gilberto Pereira , Alessio Bartocci , Martina Pannuzzo , Simone Albani QRB Discovery, 2022, 3, pp.e19. ⟨10.1017/qrd.2022.16⟩ Article dans une revue hal-03864646v1
	Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes Neila Machado , Bart Bruininks , Priyanka Singh , Laurita dos Santos , Carine Dal Pizzol 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 Souza Nature Communications, In press, 13 (1), pp.68. ⟨10.1038/s41467-021-27627-4⟩ Article dans une revue hal-03855658v1
	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
	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 Nature Chemistry, 2021, 13 (12), pp.1192-1199. ⟨10.1038/s41557-021-00824-w⟩ Article dans une revue hal-03863245v1
	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
	Martini 3: a general purpose force field for coarse-grained molecular dynamics Paulo Souza , Riccardo Alessandri , Jonathan Barnoud , Sebastian Thallmair , Ignacio Faustino Nature Methods, 2021, 18 (4), pp.382-388. ⟨10.1038/s41592-021-01098-3⟩ Article dans une revue hal-03863208v1
	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
	Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies Bart Bruininks , Albert Thie , Paulo Souza , Tsjerk Wassenaar , Shirin Faraji Journal of Chemical Theory and Computation, 2021, 17 (12), pp.7873-7885. ⟨10.1021/acs.jctc.1c00446⟩ Article dans une revue hal-03863224v1
	Protein–ligand binding with the coarse-grained Martini model Paulo C T Souza , Sebastian Thallmair , Paolo Conflitti , Carlos Ramírez-Palacios , Riccardo Alessandri Nature Communications, 2020, 11 (1), pp.3714. ⟨10.1038/s41467-020-17437-5⟩ Article dans une revue hal-04296809v1
	Titratable Martini model for constant pH simulations Fabian Grünewald , Paulo C. T. Souza , Haleh Abdizadeh , Jonathan Barnoud , Alex de Vries Journal of Chemical Physics, 2020, 153 (2), ⟨10.1063/5.0014258⟩ Article dans une revue hal-04296865v1
	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

	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 A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, AIP Publishing LLCMelville, New York, pp.1-1-1-34, 2023, ⟨10.1063/9780735425279_001⟩ Chapitre d'ouvrage hal-04305938v1

	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

Paulo Telles de Souza

Publications

Martini 3 Coarse-Grained Force Field for Cholesterol

Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG

Pragmatic Coarse-Graining of Proteins: Models and Applications

Rational Prediction of PROTAC-compatible Protein-Protein Interfaces by Molecular Docking

Identification of inhibitors targeting the energy-coupling factor (ECF) transporters

Expulsion mechanism of the substrate-translocating subunit in ECF transporters

Two decades of Martini: Better beads, broader scope

Modelling structural properties of cyanine dye nanotubes at coarse-grained level

Towards design of drugs and delivery systems with the Martini coarse-grained model

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

Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials

Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field

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

Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties

Martini 3: a general purpose force field for coarse-grained molecular dynamics

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

Protein–ligand binding with the coarse-grained Martini model

Titratable Martini model for constant pH simulations

Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction

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

A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α 1