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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, Charly Empereur-mot, Josef Melcr, Tugba N. Ozturk, Drew W. F. Bennett, Lisbeth R. Kjølbye, Christopher Brasnett, Valentina Corradi, Hanif M. Khan, Elio A. Cino, Jackson Crowley, Hyuntae Kim, Balázs Fábián, Ana C. Borges-Araújo, Giovanni M. Pavan, Fabio Lolicato, Tsjerk A. Wassenaar, Manuel N. Melo, Sebastian Thallmair, Timothy S. Carpenter, Luca Monticelli, D. Peter Tieleman, Birgit Schiøtt, Paulo C. T. Souza, Siewert J. Marrink

Version 1 posted 26 December 2024

1,237

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2

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Theoretical and Computational Chemistry

Working Paper

Pitfalls of the Martini Model

Riccardo Alessandri, Paulo C. T. Souza, Sebastian Thallmair, Manuel N. Melo, Alex H. de Vries, Siewert-Jan Marrink

Version 1 posted 16 May 2019

810

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Physical Chemistry

Working Paper

Multiscale Modeling of Molecular Structure and Optical Properties of Complex Supramolecular Aggregates

Anna S. Bondarenko, Ilias Patmanidis, Riccardo Alessandri, Paulo C. T. Souza, Thomas L.C. Jansen, Alex H. de Vries, Siewert-Jan Marrink, Jasper Knoester

Version 1 posted 01 June 2020

881

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1

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Biological and Medicinal Chemistry

Working Paper

Targeting the energy-coupling factor (ECF) transporters: identification of new tool compounds

Eleonora Diamanti, Inda Setyawati, Spyridon Bousis, Paulo C. T. Souza, leticia mojas, lotteke Swier, Jörg Haupenthal, Paddy Gibson, carsten volz, weronika stanek, manuel Jaeger, jennifer herrmann, Siewert Marrink, jan-willem veening, rolf müller, dirk J. slotboom, Anna K.H. Hirsch

Version 2 posted 01 December 2021

1,216

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5

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Analytical Chemistry

Working Paper

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-Jan Marrink, Paulo C. T. Souza

Version 1 posted 28 May 2020

680

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1

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Physical Chemistry

Working Paper

Martini 3 Coarse-Grained Force Field: Small Molecules

Riccardo Alessandri, Jonathan Barnoud, Anders S. Gertsen, Ilias Patmanidis, Alex H. de Vries, Paulo C. T. Souza, Siewert J. Marrink

Version 1 posted 19 July 2021

5,409

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Theoretical and Computational Chemistry

Working Paper

Martini 3 Coarse-Grained Force Field for cholesterol

Luís Borges-Araújo, Ana Borges-Araújo, Tugba Ozturk, Daniel P. Ramirez-Echemendia, Balázs Fábián, Timothy S. Carpenter, Sebastian Thallmair, Jonathan Barnoud, Helgi I. Ingólfsson, Gerhard Hummer, D. Peter Tieleman, Siewert J. Marrink, Paulo C. T. Souza, Manuel N. Melo

Version 2 posted 22 September 2023

1,549

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2

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Theoretical and Computational Chemistry

Working Paper

OLIVES: A Go-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, Birgit Schiøtt

Version 1 posted 17 November 2023

941

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2

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Theoretical and Computational Chemistry

Working Paper

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

Ilias Patmanidis, Paulo C. T. Souza, Selim Sami, Remco W. A. Havenith, Alex H. de Vries, Siewert J. Marrink

Version 1 posted 09 March 2022

288

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Theoretical and Computational Chemistry

Working Paper

CGCompiler: Automated coarse-grained molecule parameterization via noise-resistant mixed-variable optimization

Kai S. Stroh, Paulo C. T. Souza, Luca Monticelli, H. Jelger Risselada

Version 1 posted 13 June 2023

444

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1

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Refine Search

11 results in Paulo C. T. Souza in Authors: Paulo C. T. Souza

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

Pitfalls of the Martini Model

Multiscale Modeling of Molecular Structure and Optical Properties of Complex Supramolecular Aggregates

Targeting the energy-coupling factor (ECF) transporters: identification of new tool compounds

Martini Coarse-Grained Models of Imidazolium-Based Ionic Liquids: From Nanostructural Organization to Liquid-Liquid Extraction

Martini 3 Coarse-Grained Force Field: Small Molecules

Martini 3 Coarse-Grained Force Field for cholesterol

OLIVES: A Go-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field

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

CGCompiler: Automated coarse-grained molecule parameterization via noise-resistant mixed-variable optimization

11 results in Authors: Paulo C. T. Souza