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

Using graph neural networks to reconstruct charged pion showers in the CMS High Granularity Calorimeter

Autor: Aamir, M., Acar, B., Adamov, G., Adams, T., Adloff, C., Afanasiev, S., Agrawal, C., Ahmad, A., Ahmed, H. A., Akbar, S., Akchurin, N., Akgul, B., Akgun, B., Akpinar, R. O., Aktas, E., AlKadhim, A., Alexakhin, V., Alimena, J., Alison, J., Alpana, A., Alshehri, W., Dominguez, P. Alvarez, Alyari, M., Amendola, C., Amir, R. B., Andersen, S. B., Andreev, Y., Antoszczuk, P. D., Aras, U., Ardila, L., Aspell, P., Avila, M., Awad, I., Aydilek, O., Azimi, Z., Pretel, A. Aznar, Bach, O. A., Bainbridge, R., Bakshi, A., Bam, B., Banerjee, S., Barney, D., Bayraktar, O., Beaudette, F., Beaujean, F., Becheva, E., Behera, P. K., Belloni, A., Bergauer, T., Besancon, M., Bylund, O. Bessidskaia, Bhatt, L., Bhowmil, D., Blekman, F., Blinov, P., Bloch, P., Bodek, A., Boger, a., Bonnemaison, A., Bouyjou, F., Brennan, L., Brondolin, E., Brusamolino, A., Bubanja, I., Perraguin, A. Buchot, Bunin, P., Misura, A. Burazin, Butler-nalin, A., Cakir, A., Callier, S., Campbell, S., Canderan, K., Cankocak, K., Cappati, A., Caregari, S., Carron, S., Carty, C., Cauchois, A., Ceard, L., Cerci, S., Chang, P. J., Chatterjee, R. M., Chatterjee, S., Chattopadhyay, P., Chatzistavrou, T., Chaudhary, M. S., Chauhan, A., Chen, J. A., Chen, J., Chen, Y., Cheng, K., Cheung, H., Chhikara, J., Chiron, A., Chiusi, M., Chokheli, D., Chudasama, R., Clement, E., Mendez, S. Coco, Coko, D., Coskun, K., Couderc, F., Crossman, B., Cui, Z., Cuisset, T., Cummings, G., Curtis, E. M., D'Alfonso, M., D-hler-ball, J., Dadazhanova, O., Damgov, J., Das, I., DasGupta, S., Dauncey, P., Mendes, A. David Tinoco, Davies, G., Davignon, O., DeLa, P. deBarbaroC., DeSilva, M., DeWit, A., Debbins, P., Defranchis, M. M., Delagnes, E., Devouge, P., Dewangan, C., DiGuglielmo, G., Diehl, L., Dilsiz, K., Dincer, G. G., Dittmann, J., Dragicevic, M., Du, D., Dubinchik, B., Dugad, S., Dulucq, F., Dumanoglu, I., Duran, B., Dutta, S., Dutta, V., Dychkant, A., Dünser, M., Edberg, T., Ehle, I. T., Berni, A. El, Elias, F., Eno, S. C., Erdogan, E. N., Erkmen, B., Ershov, Y., Ertorer, E. Y., Extier, S., Eychenne, L., Fedar, Y. E., Fedi, G., De Almeida, J. P. Figueiredo De De Sá Sousa, Alves, B. A. Fontana Santos Santos, Frahm, E., Francis, K., Freeman, J., French, T., Gaede, F., Gandhi, P. K., Ganjour, S., Garcia-Bellido, A., Gastaldi, F., Gazi, L., Gecse, Z., Gerwig, H., Gevin, O., Ghosh, S., Gill, K., Gleyzer, S., Godinovic, N., Goek, M., Goettlicher, P., Goff, R., Golunov, A., Gonultas, B., Martínez, J. D. González, Gorbounov, N., Gouskos, L., Gray, A., Gray, L., Grieco, C., Groenroos, S., Groner, D., Gruber, A., Grummer, A., Grönroos, S., Guilloux, F., Guler, Y., Gungordu, A. D., Guo, J., Guo, K., Guler, E. Gurpinar, Gutti, H. K., Guvenli, A. A., Gülmez, E., Hacisahinoglu, B., Halkin, Y., Machado, G. Hamilton Ilha, Hare, H. S., Hatakeyama, K., Heering, A. H., Hegde, V., Heintz, U., Hinton, N., Hinzmann, A., Hirschauer, J., Hitlin, D., Hos, İ., Hou, B., Hou, X., Howard, A., Howe, C., Hsieh, H., Hsu, T., Hua, H., Hummer, F., Imran, M., Incandela, J., Iren, E., Isildak, B., Jackson, P. S., Jackson, W. J., Jain, S., Jana, P., Jaroslavceva, J., Jena, S., Jige, A., Jordano, P. P., Joshi, U., Kaadze, K., Kafizov, A., Kalipoliti, L., Tharayil, A. Kallil, Kaluzinska, O., Kamble, S., Kaminskiy, A., Kanemura, M., Kanso, H., Kao, Y., Kapic, A., Kapsiak, C., Karjavine, V., Karmakar, S., Karneyeu, A., Kaya, M., Topaksu, A. Kayis, Kaynak, B., Kazhykarim, Y., Khan, F. A., Khudiakov, A., Kieseler, J., Kim, R. S., Klijnsma, T., Kloiber, E. G., Klute, M., Kocak, Z., Kodali, K. R., Koetz, K., Kolberg, T., Kolcu, O. B., Komaragiri, J. R., Komm, M., Kopsalis, I., Krause, H. A., Krawczyk, M. A., Vinayakam, T. R. Krishnaswamy, Kristiansen, K., Kristic, A., Krohn, M., Kronheim, B., Krüger, K., Kudtarkar, C., Kulis, S., Kumar, M., Kumar, N., Kumar, S., Verma, R. Kumar, Kunori, S., Kunts, A., Kuo, C., Kurenkov, A., Kuryatkov, V., Kyre, S., Ladenson, J., Lamichhane, K., Landsberg, G., Langford, J., Laudrain, A., Laughlin, R., Lawhorn, J., Dortz, O. Le, Lee, S. W., Lektauers, A., Lelas, D., Leon, M., Levchuk, L., Li, A. J., Li, J., Li, Y., Liang, Z., Liao, H., Lin, K., Lin, W., Lin, Z., Lincoln, D., Linssen, L., Litomin, A., Liu, G., Liu, Y., Lobanov, A., Lohezic, V., Loiseau, T., Lu, C., Lu, R., Lu, S. Y., Lukens, P., Mackenzie, M., Magnan, A., Magniette, F., Mahjoub, A., Mahon, D., Majumder, G., Makarenko, V., Malakhov, A., Malgeri, L., Mallios, S., Mandloi, C., Mankel, A., Mannelli, M., Mans, J., Mantilla, C., Martinez, G., Massa, C., Masterson, P., Matthewman, M., Matveev, V., Mayekar, S., Mazlov, I., Mehta, A., Mestvirishvili, A., Miao, Y., Milella, G., Mirza, I. R., Mitra, P., Moccia, S., Mohanty, G. B., Monti, F., Moortgat, F., Murthy, S., Music, J., Musienko, Y., Nabili, S., Nayak, S., Nelson, J. W., Nema, A., Neutelings, I., Niedziela, J., Nikitenko, A., Noonan, D., Noy, M., Nurdan, K., Obraztsov, S., Ochando, C., Ogul, H., Olsson, J., Onel, Y., Ozkorucuklu, S., Paganis, E., Palit, P., Pan, R., Pandey, S., Pantaleo, F., Papageorgakis, C., Paramesvaran, S., Paranjpe, M. M., Parolia, S., Parsons, A. G., Parygin, P., Paulini, M., Paus, C., Peñaló, K., Pedro, K., Pekic, V., Peltola, T., Peng, B., Perego, A., Perini, D., Petrilli, A., Pham, H., Pierre-Emile, T., Podem, S. K., Popov, V., Portales, L., Potok, O., Pradeep, P. B., Pramanik, R., Prosper, H., Prvan, M., Qasim, S. R., Qu, H., Quast, T., Trivino, A. Quiroga, Rabour, L., Raicevic, N., Rajpoot, H., Rao, M. A., Rapacz, K., Redjeb, W., Reinecke, M., Revering, M., Roberts, A., Rohlf, J., Rosado, P., Rose, A., Rothman, S., Rout, P. K., Rovere, M., Rumerio, P., Rusack, R., Rygaard, L., Ryjov, V., Sadivnycha, S., Sahin, M. Ö., Sakarya, U., Salerno, R., Saradhy, R., Saraf, M., Sarbandi, K., Sarkisla, M. A., Satyshev, I., Saud, N., Sauvan, J., Schindler, G., Schmidt, A., Schmidt, I., Schmitt, M. H., Sculac, A., Sculac, T., Sedelnikov, A., Seez, C., Sefkow, F., Selivanova, D., Selvaggi, M., Sergeychik, V., Sert, H., Shahid, M., Sharma, P., Sharma, R., Sharma, S., Shelake, M., Shenai, A., Shih, C. W., Shinde, R., Shmygol, D., Shukla, R., Sicking, E., Silva, P., Simsek, C., Simsek, E., Sirasva, B. K., Sirois, Y., Song, S., Song, Y., Soudais, G., Sriram, S., StJacques, R. R., StahlLeiton, A. G., Steen, A., Stein, J., Strait, J., Strobbe, N., Su, X., Sukhov, E., Suleiman, A., Cerci, D. Sunar, Suryadevara, P., Swain, K., Syal, C., Tali, B., Tanay, K., Tang, W., Tanvir, A., Tao, J., Tarabini, A., Tatli, T., Taylor, R., Taysi, Z. C., Teafoe, G., Tee, C. Z., Terrill, W., Thienpont, D., Thomas, R., Titov, M., Todd, C., Todd, E., Toms, M., Tosun, A., Troska, J., Tsai, L., Tsamalaidze, Z., Tsionou, D., Tsipolitis, G., Tsirigoti, M., Tu, R., Polat, S. N. Tural, Undleeb, S., Usai, E., Uslan, E., Ustinov, V., Vernazza, E., Viahin, O., Viazlo, O., Vichoudis, P., Vijay, A., Virdee, T., Voirin, E., Vojinovic, M., Voytishin, N., Vámi, T. Á., Wade, A., Walter, D., Wang, C., Wang, F., Wang, J., Wang, K., Wang, X., Wang, Y., Wang, Z., Wanlin, E., Wayne, M., Wetzel, J., Whitbeck, A., Wickwire, R., Wilmot, D., Wilson, J., Wu, H., Xiao, M., Yang, J., Yazici, B., Ye, Y., Yetkin, T., Yi, R., Yohay, R., Yu, T., Yuan, C., Yuan, X., Yuksel, O., YushmanoV, I., Yusuff, I., Zabi, A., Zareckis, D., Zarubin, A., Zehetner, P., Zghiche, A., Zhang, C., Zhang, D., Zhang, H., Zhang, J., Zhang, Z., Zhao, X., Zhong, J., Zhou, Y., Zorbilmez, Ç.

A novel method to reconstruct the energy of hadronic showers in the CMS High Granularity Calorimeter (HGCAL) is presented. The HGCAL is a sampling calorimeter with very fine transverse and longitudinal granularity. The active media are silicon sensor

Externí odkaz: http://arxiv.org/abs/2406.11937

AntiFold: Improved antibody structure-based design using inverse folding

Autor: Høie, Magnus Haraldson, Hummer, Alissa, Olsen, Tobias H., Aguilar-Sanjuan, Broncio, Nielsen, Morten, Deane, Charlotte M.

The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining structura

Externí odkaz: http://arxiv.org/abs/2405.03370

A non-cubic space-filling modular robot

Autor: Hummer, Tyler, Kriegman, Sam

Space-filling building blocks of diverse shape permeate nature at all levels of organization, from atoms to honeycombs, and have proven useful in artificial systems, from molecular containers to clay bricks. But, despite the wide variety of space-fil

Externí odkaz: http://arxiv.org/abs/2403.01323

Targeting NLRP3 inhibits AML progression by inducing PERK/eIF2-mediated apoptosis

Autor: Michela Luciano, Helene Sieberer, Peter W. Krenn, Hieu-Hoa Dang, Julia Vetter, Theresa Neuper, Diana Amend, Constantin Blöchl, Christian X. Weichenberger, Anna Eglseer, Michael S. Unger, Ancuela Andosch, Philip Steiner, Daniel Neureiter, Renate Bauer, Laura Hummer, Suzana Tesanovic, Stephanie Binder, Dominik P. Elmer, Helen Strandt, Susanne Schaller, Dirk Strunk, Lisa Pleyer, Richard Greil, Stephan Winkler, Tanja N. Hartmann, Dirk Schmidt-Arras, Christian G. Huber, Fritz Aberger, Jutta Horejs-Hoeck

Publikováno v: Cell Communication and Signaling, Vol 22, Iss 1, Pp 1-14 (2024)

Abstract Background Acute myeloid leukemia (AML) is characterized by the abnormal proliferation of myeloid precursor cells and presents significant challenges in treatment due to its heterogeneity. Recently, the NLRP3 inflammasome has emerged as a po

Externí odkaz: https://doaj.org/article/4d77e7ab0fdf4883bc818ffc7dd4f0d8