Search Results - "Souza, Paulo C.T."

Computational Modeling of Realistic Cell Membranes by Marrink, Siewert J, Corradi, Valentina, Souza, Paulo C.T, Ingólfsson, Helgi I, Tieleman, D. Peter, Sansom, Mark S.P

“…Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in…”
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A Practical View of the Martini Force Field by Bruininks, Bart M H, Souza, Paulo C T, Marrink, Siewert J

“…Martini is a coarse-grained (CG) force field suitable for molecular dynamics (MD) simulations of (bio)molecular systems. It is based on mapping of two to four…”
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Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants by Souza, Paulo C.T., Barra, Gustavo B., Velasco, Lara F.R., Ribeiro, Isabel C.J., Simeoni, Luiz A., Togashi, Marie, Webb, Paul, Neves, Francisco A.R., Skaf, Munir S., Martínez, Leandro, Polikarpov, Igor

“…Nuclear hormone receptors (NRs) form a family of transcription factors that mediate cellular responses initiated by hormone binding. It is generally recognized…”
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Transmembrane region dimer structures of Type 1 receptors readily sample alternate configurations: MD simulations using the Martini 3 coarse grained model compared to AlphaFold2 Multimer by Sahoo, Amita R, Souza, Paulo C.T., Meng, Zhiyuan, Buck, Matthias

“…Determination of the structure and dynamics of transmembrane (TM) regions of singletransmembrane receptors is key to understanding their mechanism of signal…”
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Two decades of Martini: Better beads, broader scope by Marrink, Siewert J., Monticelli, Luca, Melo, Manuel N., Alessandri, Riccardo, Tieleman, D. Peter, Souza, Paulo C. T.

“…The Martini model, a coarse‐grained force field for molecular dynamics simulations, has been around for nearly two decades. Originally developed for…”
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Pitfalls of the Martini Model by Alessandri, Riccardo, Souza, Paulo C. T, Thallmair, Sebastian, Melo, Manuel N, de Vries, Alex H, Marrink, Siewert J

“…The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current computational modeling…”
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Protein–ligand binding with the coarse-grained Martini model by Souza, Paulo C. T., Thallmair, Sebastian, Conflitti, Paolo, Ramírez-Palacios, Carlos, Alessandri, Riccardo, Raniolo, Stefano, Limongelli, Vittorio, Marrink, Siewert J.

“…The detailed understanding of the binding of small molecules to proteins is the key for the development of novel drugs or to increase the acceptance of…”
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Enhancing Molecular n‐Type Doping of Donor–Acceptor Copolymers by Tailoring Side Chains by 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

“…In this contribution, for the first time, the molecular n‐doping of a donor–acceptor (D–A) copolymer achieving 200‐fold enhancement of electrical conductivity…”
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CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization by Stroh, Kai Steffen, Souza, Paulo C. T., Monticelli, Luca, Risselada, Herre Jelger

“…Coarse-grained force fields (CG FFs) such as the Martini model entail a predefined, fixed set of Lennard-Jones parameters (building blocks) to model virtually…”
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High performance collision cross section calculation—HPCCS by Zanotto, Leandro, Heerdt, Gabriel, Souza, Paulo C. T., Araujo, Guido, Skaf, Munir S.

“…Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM‐MS) devices in 2003, a large number of research laboratories have embraced…”
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Assessing the Martini 3 protein model: A review of its path and potential by Borges-Araújo, Luís, Pereira, Gilberto P., Valério, Mariana, Souza, Paulo C.T.

“…Coarse-grained (CG) protein models have become indispensable tools for studying many biological protein details, from conformational dynamics to the…”
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Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer by Sahoo, Amita R., Souza, Paulo C.T., Meng, Zhiyuan, Buck, Matthias

“…Structures and dynamics of transmembrane (TM) receptor regions are key to understanding their signaling mechanism across membranes. Here we examine…”
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Polyply; a python suite for facilitating simulations of macromolecules and nanomaterials by Grünewald, Fabian, Alessandri, Riccardo, Kroon, Peter C., Monticelli, Luca, Souza, Paulo C. T., Marrink, Siewert J.

“…Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However,…”
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Facilitating CG Simulations with MAD: The MArtini Database Server by Hilpert, Cécile, Beranger, Louis, Souza, Paulo C. T., Vainikka, Petteri A., Nieto, Vincent, Marrink, Siewert J., Monticelli, Luca, Launay, Guillaume

“…The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the…”
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Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation by Ingólfsson, Helgi I, Rizuan, Azamat, Liu, Xikun, Mohanty, Priyesh, Souza, Paulo C.T., Marrink, Siewert J, Bowers, Michael T, Mittal, Jeetain, Berry, Joel

“…The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as…”
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Improved Parameterization of Phosphatidylinositide Lipid Headgroups for the Martini 3 Coarse-Grain Force Field by Borges-Araújo, Luís, Souza, Paulo C. T, Fernandes, Fábio, Melo, Manuel N

“…Phosphoinositides are a family of membrane phospholipids that play crucial roles in membrane regulatory events. As such, these lipids are often a key part of…”
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Automatic Optimization of Lipid Models in the Martini Force Field Using SwarmCG by Empereur-mot, Charly, Pedersen, Kasper B., Capelli, Riccardo, Crippa, Martina, Caruso, Cristina, Perrone, Mattia, Souza, Paulo C. T., Marrink, Siewert J., Pavan, Giovanni M.

“…After two decades of continued development of the Martini coarse-grained force field (CG FF), further refinment of the already rather accurate Martini lipid…”
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Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field by Khan, Hanif M, Souza, Paulo C. T, Thallmair, Sebastian, Barnoud, Jonathan, de Vries, Alex H, Marrink, Siewert J, Reuter, Nathalie

“…Cation−π interactions play an important role in biomolecular recognition, including interactions between membrane phosphatidylcholine lipids and aromatic amino…”
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An implementation of the Martini coarse-grained force field in OpenMM by MacCallum, Justin L., Hu, Shangnong, Lenz, Stefan, Souza, Paulo C.T., Corradi, Valentina, Tieleman, D. Peter

“…We describe a complete implementation of Martini 2 and Martini 3 in the OpenMM molecular dynamics software package. Martini is a widely used coarse-grained…”
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Martini 3 Coarse‐Grained Force Field: Small Molecules by Alessandri, Riccardo, Barnoud, Jonathan, Gertsen, Anders S., Patmanidis, Ilias, de Vries, Alex H., Souza, Paulo C. T., Marrink, Siewert J.

“…The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved the accuracy of the model in predicting molecular packing and…”
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