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

Structural basis for antibiotic transport and inhibition in PepT2

Autor: Joanne L. Parker, Justin C. Deme, Simon M. Lichtinger, Gabriel Kuteyi, Philip C. Biggin, Susan M. Lea, Simon Newstead

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)

Abstract The uptake and elimination of beta-lactam antibiotics in the human body are facilitated by the proton-coupled peptide transporters PepT1 (SLC15A1) and PepT2 (SLC15A2). The mechanism by which SLC15 family transporters recognize and discrimina

Externí odkaz: https://doaj.org/article/66b1ac35c95b49cdb878067a8315deb4

The mechanism of mammalian proton-coupled peptide transporters

Autor: Simon M Lichtinger, Joanne L Parker, Simon Newstead, Philip C Biggin

Publikováno v: eLife, Vol 13 (2024)

Proton-coupled oligopeptide transporters (POTs) are of great pharmaceutical interest owing to their promiscuous substrate binding site that has been linked to improved oral bioavailability of several classes of drugs. Members of the POT family are co

Externí odkaz: https://doaj.org/article/a81effb883ee4d87878995426199639c

Mobility and strength training with and without protein supplements for pre-frail or frail older adults with low protein intake: the Maximising Mobility and Strength Training (MMoST) feasibility randomised controlled trial protocol [version 2; peer review: 2 approved]

Autor: Caoileann Murphy, Alana Morris, Nirvana Croft, Andrew Carver, Esther Williamson, Kavita Biggin, Sarah E. Lamb, Ioana R. Marian

Publikováno v: NIHR Open Research, Vol 3 (2024)

Background Frailty is a common syndrome affecting older people and puts them at risk of hospitalisation, needing care or death. First signs of frailty include reduced muscle strength and mobility decline. A key cause of mobility decline as we age is

Externí odkaz: https://doaj.org/article/6ba6c564ac4d4fcf90b52b59c23e43a4

Discovering patterns in outpatient neurology appointments using state sequence analysis

Autor: Fran Biggin, Quinta Ashcroft, Timothy Howcroft, Jo Knight, Hedley Emsley

Publikováno v: BMC Health Services Research, Vol 23, Iss 1, Pp 1-13 (2023)

Abstract Background Outpatient services in the UK, and in particular outpatient neurology services, are under considerable pressure with an ever-increasing gap between capacity and demand. To improve services, we first need to understand the current

Externí odkaz: https://doaj.org/article/25083dba3f6a40408dcdc1dc955f0d2f