CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands

por Mottin, Melina, Souza, Paulo C. T., Ricci, Clarisse G., Skaf, Munir S.
Publicado 2016

An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation

por Souza, Paulo C. T., Thallmair, Sebastian, Marrink, Siewert J., Mera-Adasme, Raúl
Publicado 2019

Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations

por Souza, Paulo C. T., Limongelli, Vittorio, Wu, Sangwook, Marrink, Siewert J., Monticelli, Luca
Publicado 2021

An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position

por Souza, Paulo C. T., Textor, Larissa C., Melo, Denise C., Nascimento, Alessandro S., Skaf, Munir S., Polikarpov, Igor
Publicado 2017

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

por Grünewald, Fabian, Alessandri, Riccardo, Kroon, Peter C., Monticelli, Luca, Souza, Paulo C. T., Marrink, Siewert J.
Publicado 2022

Pitfalls of the Martini Model

por Alessandri, Riccardo, Souza, Paulo C. T., Thallmair, Sebastian, Melo, Manuel N., de Vries, Alex H., Marrink, Siewert J.
Publicado 2019

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

por Tsanai, Maria, Frederix, Pim W. J. M., Schroer, Carsten F. E., Souza, Paulo C. T., Marrink, Siewert J.
Publicado 2021

Sequential Voxel-Based Leaflet Segmentation of Complex Lipid Morphologies

por Bruininks, Bart M. H., Thie, Albert S., Souza, Paulo C. T., Wassenaar, Tsjerk A., Faraji, Shirin, Marrink, Siewert J.
Publicado 2021

Computational Modeling of Realistic Cell Membranes

por Marrink, Siewert J., Corradi, Valentina, Souza, Paulo C.T., Ingólfsson, Helgi I., Tieleman, D. Peter, Sansom, Mark S.P.
Publicado 2019

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

por Patmanidis, Ilias, Souza, Paulo C. T., Sami, Selim, Havenith, Remco W. A., de Vries, Alex H., Marrink, Siewert J.
Publicado 2022

Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field

por Khan, Hanif M., Souza, Paulo C. T., Thallmair, Sebastian, Barnoud, Jonathan, de Vries, Alex H., Marrink, Siewert J., Reuter, Nathalie
Publicado 2020

Protein–ligand binding with the coarse-grained Martini model

por Souza, Paulo C. T., Thallmair, Sebastian, Conflitti, Paolo, Ramírez-Palacios, Carlos, Alessandri, Riccardo, Raniolo, Stefano, Limongelli, Vittorio, Marrink, Siewert J.
Publicado 2020

Membrane mediated toppling mechanism of the folate energy coupling factor transporter

por Faustino, Ignacio, Abdizadeh, Haleh, Souza, Paulo C. T., Jeucken, Aike, Stanek, Weronika K., Guskov, Albert, Slotboom, Dirk J., Marrink, Siewert J.
Publicado 2020

Expulsion mechanism of the substrate-translocating subunit in ECF transporters

por Thangaratnarajah, Chancievan, Nijland, Mark, Borges-Araújo, Luís, Jeucken, Aike, Rheinberger, Jan, Marrink, Siewert J., Souza, Paulo C. T., Paulino, Cristina, Slotboom, Dirk J.
Publicado 2023

Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates

por Bondarenko, Anna S., Patmanidis, Ilias, Alessandri, Riccardo, Souza, Paulo C. T., Jansen, Thomas L. C., de Vries, Alex H., Marrink, Siewert J., Knoester, Jasper
Publicado 2020

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

por Empereur-mot, Charly, Pedersen, Kasper B., Capelli, Riccardo, Crippa, Martina, Caruso, Cristina, Perrone, Mattia, Souza, Paulo C. T., Marrink, Siewert J., Pavan, Giovanni M.
Publicado 2023

A new integrative weaning index of discontinuation from mechanical ventilation

por Nemer, Sergio N, Barbas, Carmen SV, Caldeira, Jefferson B, Cárias, Thiago C, Santos, Ricardo G, Almeida, Luiz C, Azeredo, Leandro M, Noé, Rosângela A, Guimarães, Bruno S, Souza, Paulo C
Publicado 2009

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

por Kjølbye, Lisbeth R., Pereira, Gilberto P., Bartocci, Alessio, Pannuzzo, Martina, Albani, Simone, Marchetto, Alessandro, Jiménez-García, Brian, Martin, Juliette, Rossetti, Giulia, Cecchini, Marco, Wu, Sangwook, Monticelli, Luca, Souza, Paulo C. T.
Publicado 2022

Martini 3 Coarse-Grained Force Field for Carbohydrates

por Grünewald, Fabian, Punt, Mats H., Jefferys, Elizabeth E., Vainikka, Petteri A., König, Melanie, Virtanen, Valtteri, Meyer, Travis A., Pezeshkian, Weria, Gormley, Adam J., Karonen, Maarit, Sansom, Mark S. P., Souza, Paulo C. T., Marrink, Siewert J.
Publicado 2022

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

por Diamanti, Eleonora, Souza, Paulo C. T., Setyawati, Inda, Bousis, Spyridon, Gómez, Leticia M., Swier, Lotteke J.Y.M., Shams, Atanaz, Tsarenko, Aleksei, Stanek, Weronika K., Jäger, Manuel, Marrink, Siewert J., Slotboom, Dirk J., Hirsch, Anna K. H.
Publicado 2023