The need to implement FAIR principles in biomolecular simulations

Autor: Amaro, Rommie, Åqvist, Johan, Bahar, Ivet, Battistini, Federica, Bellaiche, Adam, Beltran, Daniel, Biggin, Philip C., Bonomi, Massimiliano, Bowman, Gregory R., Bryce, Richard, Bussi, Giovanni, Carloni, Paolo, Case, David, Cavalli, Andrea, Chang, Chie-En A., Cheatham III, Thomas E., Cheung, Margaret S., Chipot, Cris, Chong, Lillian T., Choudhary, Preeti, Cisneros, Gerardo Andres, Clementi, Cecilia, Collepardo-Guevara, Rosana, Coveney, Peter, Covino, Roberto, Crawford, T. Daniel, Peraro, Matteo Dal, de Groot, Bert, Delemotte, Lucie, De Vivo, Marco, Essex, Jonathan, Fraternali, Franca, Gao, Jiali, Gelpí, Josep Lluís, Gervasio, Francesco Luigi, Gonzalez-Nilo, Fernando Danilo, Grubmüller, Helmut, Guenza, Marina, Guzman, Horacio V., Harris, Sarah, Head-Gordon, Teresa, Hernandez, Rigoberto, Hospital, Adam, Huang, Niu, Huang, Xuhui, Hummer, Gerhard, Iglesias-Fernández, Javier, Jensen, Jan H., Jha, Shantenu, Jiao, Wanting, Jorgensen, William L., Kamerlin, Shina Caroline Lynn, Khalid, Syma, Laughton, Charles, Levitt, Michael, Limongelli, Vittorio, Lindahl, Erik, Lindorff-Larsen, Kresten, Loverde, Sharon, Lundborg, Magnus, Luo, Yun Lyna, Luque, Francisco Javier, Lynch, Charlotte I., MacKerell, Alexander, Magistrato, Alessandra, Marrink, Siewert J., Martin, Hugh, McCammon, J. Andrew, Merz, Kenneth, Moliner, Vicent, Mulholland, Adrian, Murad, Sohail, Naganathan, Athi N., Nangia, Shikha, Noe, Frank, Noy, Agnes, Oláh, Julianna, O'Mara, Megan, Ondrechen, Mary Jo, Onuchic, José N., Onufriev, Alexey, Osuna, Silvia, Panchenko, Anna R., Pantano, Sergio, Parish, Carol, Parrinello, Michele, Perez, Alberto, Perez-Acle, Tomas, Perilla, Juan R., Pettitt, B. Montgomery, Pietropalo, Adriana, Piquemal, Jean-Philip, Poma, Adolfo, Praprotnik, Matej, Ramos, Maria J., Ren, Pengyu, Reuter, Nathalie, Roitberg, Adrian, Rosta, Edina, Rovira, Carme, Roux, Benoit, Röthlisberger, Ursula, Sanbonmatsu, Karissa Y., Schlick, Tamar, Shaytan, Alexey K., Simmerling, Carlos, Smith, Jeremy C., Sugita, Yuji, Świderek, Katarzyna, Taiji, Makoto, Tao, Peng, Tikhonova, Irina G., Tirado-Rives, Julian, Tunón, Inaki, Van Der Kamp, Marc W., Van der Spoel, David, Velankar, Sameer, Voth, Gregory A., Wade, Rebecca, Warshel, Ariel, Welborn, Valerie Vaissier, Wetmore, Stacey, Wong, Chung F., Yang, Lee-Wei, Zacharias, Martin, Orozco, Modesto

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a data

Externí odkaz: http://arxiv.org/abs/2407.16584

Targeting the conserved active site of splicing machines with specific and selective small molecule modulators

Autor: Ilaria Silvestri, Jacopo Manigrasso, Alessandro Andreani, Nicoletta Brindani, Caroline Mas, Jean-Baptiste Reiser, Pietro Vidossich, Gianfranco Martino, Andrew A. McCarthy, Marco De Vivo, Marco Marcia

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-15 (2024)

Abstract The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation

Externí odkaz: https://doaj.org/article/c7fe2568740c4dfbb4808801055111e5

Tumor growth-arrest effect of tetrahydroquinazoline-derivative human topoisomerase II-alpha inhibitor in HPV-negative head and neck squamous cell carcinoma

Autor: Patrizia Sarogni, Nicoletta Brindani, Agata Zamborlin, Alessandra Gonnelli, Michele Menicagli, Ana Katrina Mapanao, Federico Munafò, Marco De Vivo, Valerio Voliani

Publikováno v: Scientific Reports, Vol 14, Iss 1, Pp 1-10 (2024)

Abstract Oral malignancies continue to have severe morbidity with less than 50% long-term survival despite the advancement in the available therapies. There is a persisting demand for new approaches to establish more efficient strategies for their tr

Externí odkaz: https://doaj.org/article/c10e6e954fdd4079a96c1211bb80dcb5

The Miraculous Madonna of Pistoia in a Devotional Replica of 1490–1500 Attributed to Niccolò di Mariano

Autor: Machtelt Brüggen Israëls, Giulia Sara de Vivo

Publikováno v: The Rijksmuseum Bulletin, Vol 72, Iss 3 (2024)

In this article, it is suggested that a small panel of the Madonna of Humility in the collection of the Rijksmuseum, executed with fifteenth-century woodworking and painting techniques and materials, is a devotional copy of the fresco of the Virgin o

Externí odkaz: https://doaj.org/article/4796cb1dba8e433cabfd78b2544fe762

Spin and charge transport in ferromagnet-superconductor-ferromagnet heterostructures: Stoner versus spin mass mismatch mechanism

Autor: Gentile, Paola, Catapano, Marilena, De Vivo, Nicola, Cuoco, Mario, Romano, Alfonso, Noce, Canio

Publikováno v: Physical Review B 105, 214501 (2022)

We study transport phenomena through a ballistic ferromagnet-superconductor-ferromagnet (F/S/F) junction, comparing the case in which the ferromagnetic order in the two F layers is of the standard Stoner type with the case where it is driven by a spi

Externí odkaz: http://arxiv.org/abs/2206.03335