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

The G\=oMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes

Autor: Cofas-Vargas, Luis F., Moreira, Rodrigo A., Poblete, Simón, Chwastyk, Mateusz, Poma, Adolfo B.

We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensi

Externí odkaz: http://arxiv.org/abs/2311.08174

First records of three species of Lasiurus Gray, 1831 (Chiroptera, Vespertilionidae) in Bolivia

Autor: Luis H. Acosta S., José L. Poma-Urey, Kathrin Barboza-Marquez, Kathia Rivero, José Ochoa-G., Jorge Salazar-Bravo

Publikováno v: Check List, Vol 20, Iss 5, Pp 1054-1066 (2024)

Insectivorous bats of the family Vespertilionidae have been grouped into eight tribes, with Lasiurini showing an extensive distribution in South America. In Bolivia, three species of lasiurine bats have been reported: Lasiurus blossevillii (Lesson &

Externí odkaz: https://doaj.org/article/7ccc760a42bb4dda8d25872f303994c2

Cox rings of blow-ups of multiprojective spaces

Autor: Bolognesi, Michele, Massarenti, Alex, Poma, Elena

Let $X^{1,n}_r$ be the blow-up of $\mathbb{P}^1\times\mathbb{P}^n$ in $r$ general points. We describe the Mori cone of $X^{1,n}_r$ for $r\leq n+2$ and for $r = n+3$ when $n\leq 4$. Furthermore, we prove that $X^{1,n}_{n+1}$ is log Fano and give an ex

Externí odkaz: http://arxiv.org/abs/2308.11283

Expanding the knowledge of the bat fauna of the Brazilian Caatinga: new geographical records of molossid bats (Chiroptera, Molossidae) for the Chapada Diamantina region, with taxonomic notes

Autor: Franger J. García, José Ochoa-G, José L. Poma-Urey, Bruce W. Miller, Fábio C. Falcão, Martín Roberto del Valle Alvarez

Publikováno v: ZooKeys, Vol 1210, Iss , Pp 333-371 (2024)

The Caatinga, an exclusive biome in Brazil, is the largest tropical dry forest area in the Americas. It is characterized by a semi-arid climate and various soils that harbor a great diversity of flora and fauna. Novel records of aerial insectivorous

Externí odkaz: https://doaj.org/article/48d76cc6f5ed4a70b9e41b312b2c41c9