Martini 3: a general purpose force field for coarse-grained molecular dynamics
Souza, Paulo C. T., Alessandri, Riccardo, Barnoud, Jonathan, Thallmair, Sebastian, Faustino, Ignacio, Grünewald, Fabian, Patmanidis, Ilias, Abdizadeh, Haleh, Bruininks, Bart M. H., Wassenaar, Tsjerk A., Kroon, Peter C., Melcr, Josef, Nieto, Vincent, Corradi, Valentina, Khan, Hanif M., Domański, Jan, Javanainen, Matti, Martinez-Seara, Hector, Reuter, Nathalie, Best, Robert B., Vattulainen, Ilpo, Monticelli, Luca, Periole, Xavier, Tieleman, D. Peter, de Vries, Alex H., Marrink, Siewert J.
Published in Nature methods (01.04.2021)
Published in Nature methods (01.04.2021)
Get full text
Journal Article
Protein–ligand binding with the coarse-grained Martini model
Souza, Paulo C. T., Thallmair, Sebastian, Conflitti, Paolo, Ramírez-Palacios, Carlos, Alessandri, Riccardo, Raniolo, Stefano, Limongelli, Vittorio, Marrink, Siewert J.
Published in Nature communications (24.07.2020)
Published in Nature communications (24.07.2020)
Get full text
Journal Article
Pitfalls of the Martini Model
Alessandri, Riccardo, Souza, Paulo C. T, Thallmair, Sebastian, Melo, Manuel N, de Vries, Alex H, Marrink, Siewert J
Published in Journal of chemical theory and computation (08.10.2019)
Published in Journal of chemical theory and computation (08.10.2019)
Get full text
Journal Article
Computational Modeling of Realistic Cell Membranes
Marrink, Siewert J, Corradi, Valentina, Souza, Paulo C.T, Ingólfsson, Helgi I, Tieleman, D. Peter, Sansom, Mark S.P
Published in Chemical reviews (08.05.2019)
Published in Chemical reviews (08.05.2019)
Get full text
Journal Article
Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid-liquid extraction
Vazquez-Salazar, Luis Itza, Selle, Michele, de Vries, Alex H, Marrink, Siewert J, Souza, Paulo C. T
Published in Green chemistry : an international journal and green chemistry resource : GC (01.01.2020)
Published in Green chemistry : an international journal and green chemistry resource : GC (01.01.2020)
Get full text
Journal Article
Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field
Khan, Hanif M, Souza, Paulo C. T, Thallmair, Sebastian, Barnoud, Jonathan, de Vries, Alex H, Marrink, Siewert J, Reuter, Nathalie
Published in Journal of chemical theory and computation (14.04.2020)
Published in Journal of chemical theory and computation (14.04.2020)
Get full text
Journal Article
An Allosteric Pathway in Copper, Zinc Superoxide Dismutase Unravels the Molecular Mechanism of the G93A Amyotrophic Lateral Sclerosis-Linked Mutation
Souza, Paulo C. T, Thallmair, Sebastian, Marrink, Siewert J, Mera-Adasme, Raúl
Published in The journal of physical chemistry letters (19.12.2019)
Published in The journal of physical chemistry letters (19.12.2019)
Get full text
Journal Article
Expulsion mechanism of the substrate-translocating subunit in ECF transporters
Thangaratnarajah, Chancievan, Nijland, Mark, Borges-Araújo, Luís, Jeucken, Aike, Rheinberger, Jan, Marrink, Siewert J., Souza, Paulo C. T., Paulino, Cristina, Slotboom, Dirk J.
Published in Nature communications (25.07.2023)
Published in Nature communications (25.07.2023)
Get full text
Journal Article
Enhancing Molecular n‐Type Doping of Donor–Acceptor Copolymers by Tailoring Side Chains
Liu, Jian, Qiu, Li, Alessandri, Riccardo, Qiu, Xinkai, Portale, Giuseppe, Dong, JingJin, Talsma, Wytse, Ye, Gang, Sengrian, Aprizal Akbar, Souza, Paulo C. T., Loi, Maria Antonietta, Chiechi, Ryan C., Marrink, Siewert J., Hummelen, Jan C., Koster, L. Jan Anton
Published in Advanced materials (Weinheim) (01.02.2018)
Published in Advanced materials (Weinheim) (01.02.2018)
Get full text
Journal Article
Membrane mediated toppling mechanism of the folate energy coupling factor transporter
Faustino, Ignacio, Abdizadeh, Haleh, Souza, Paulo C. T., Jeucken, Aike, Stanek, Weronika K., Guskov, Albert, Slotboom, Dirk J., Marrink, Siewert J.
Published in Nature communications (09.04.2020)
Published in Nature communications (09.04.2020)
Get full text
Journal Article
Multiscale modeling of molecular structure and optical properties of complex supramolecular aggregates
Bondarenko, Anna S, Patmanidis, Ilias, Alessandri, Riccardo, Souza, Paulo C. T, Jansen, Thomas L. C, de Vries, Alex H, Marrink, Siewert J, Knoester, Jasper
Published in Chemical science (Cambridge) (04.11.2020)
Published in Chemical science (Cambridge) (04.11.2020)
Get full text
Journal Article
Complex nanoemulsion for vitamin delivery: droplet organization and interaction with skin membranes
Machado, Neila, Bruininks, Bart M. H, Singh, Priyanka, dos Santos, Laurita, Dal Pizzol, Carine, Dieamant, Gustavo de C, Kruger, Odivania, Martin, Airton A, Marrink, Siewert J, Souza, Paulo C. T, Favero, Priscila P
Published in Nanoscale (06.01.2022)
Published in Nanoscale (06.01.2022)
Get full text
Journal Article
Medium chain fatty acids are selective peroxisome proliferator activated receptor (PPAR) γ activators and pan-PPAR partial agonists
Liberato, Marcelo Vizoná, Nascimento, Alessandro S, Ayers, Steven D, Lin, Jean Z, Cvoro, Aleksandra, Silveira, Rodrigo L, Martínez, Leandro, Souza, Paulo C T, Saidemberg, Daniel, Deng, Tuo, Amato, Angela Angelica, Togashi, Marie, Hsueh, Willa A, Phillips, Kevin, Palma, Mário Sérgio, Neves, Francisco A R, Skaf, Munir S, Webb, Paul, Polikarpov, Igor
Published in PloS one (23.05.2012)
Published in PloS one (23.05.2012)
Get full text
Journal Article
Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
Diamanti, Eleonora, Souza, Paulo C. T., Setyawati, Inda, Bousis, Spyridon, Monjas, Leticia, Swier, Lotteke J.Y.M., Shams, Atanaz, Tsarenko, Aleksei, Stanek, Weronika K., Jäger, Manuel, Marrink, Siewert J., Slotboom, Dirk J., Hirsch, Anna K. H.
Published in Communications biology (20.11.2023)
Published in Communications biology (20.11.2023)
Get full text
Journal Article
Author Correction: Identification of inhibitors targeting the energy-coupling factor (ECF) transporters
Diamanti, Eleonora, Souza, Paulo C. T., Setyawati, Inda, Bousis, Spyridon, Monjas, Leticia, Swier, Lotteke J.Y.M., Shams, Atanaz, Tsarenko, Aleksei, Stanek, Weronika K., Jäger, Manuel, Marrink, Siewert J., Slotboom, Dirk J., Hirsch, Anna K. H.
Published in Communications biology (09.01.2024)
Published in Communications biology (09.01.2024)
Get full text
Journal Article