The need to implement FAIR principles in biomolecular simulations

Authors: 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

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2407.16584

IFN-γ-dependent regulation of intestinal epithelial homeostasis by NKT cells

Authors: Lebrusant-Fernandez, Marta ^{1, 2, 5}, ap Rees, Tom ^{1, 2, 5}, Jimeno, Rebeca ^{1, 2, 6}, Angelis, Nikolaos ², Ng, Joseph C. ^{3, 4}, Fraternali, Franca ^{3, 4}, Li, Vivian S.W. ², Barral, Patricia ^{1, 2, 7, ∗}

Source: In Cell Reports 24 December 2024 43(12)

Modelling the assembly and flexibility of antibody structures

Authors: Guo, Dongjun, De Sciscio, Maria Laura, Chi-Fung Ng, Joseph, Fraternali, Franca

Source: In Current Opinion in Structural Biology February 2024 84

Roles of repertoire diversity in robustness of humoral immune response

Authors: Mozeika, Alexander, Fraternali, Franca, Dunn-Walters, Deborah, Coolen, Anthony C. C.

Subject Terms: Quantitative Biology - Cell Behavior, Condensed Matter - Disordered Systems and Neural Networks, Physics - Biological Physics

Access URL: http://arxiv.org/abs/1910.13357

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In Silico and In Vitro Analysis of IL36RN Alterations Reveals Critical Residues for the Function of the Interleukin-36 Receptor Complex

Authors: Hassi, Niina K., Weston, Timir, Rinaldi, Giulia, Ng, Joseph C., Smahi, Asma, Twelves, Sophie, Davan-Wetton, Camilla, Fakhreddine, Dana, Fraternali, Franca, Capon, Francesca

Source: In Journal of Investigative Dermatology June 2023

Structural and energetic analyses of SARS-CoV-2 N-terminal domain characterise sugar binding pockets and suggest putative impacts of variants on COVID-19 transmission

Authors: Lam, Su Datt, Waman, Vaishali P., Fraternali, Franca, Orengo, Christine, Lees, Jonathan

Source: Computational and Structural Biotechnology Journal. 20:6302-6316

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190062628.0x000001&indx=1&recIds=ETOCvdc_100190062628.0x000001

Allosteric Regulation of the Soluble Epoxide Hydrolase by Nitro Fatty Acids: a Combined Experimental and Computational Approach

Authors: Qiu, Qiongju, Abis, Giancarlo, Mattingly-Peck, Florence, Lynham, Steven, Fraternali, Franca, Conte, Maria R

Source: In Journal of Molecular Biology 15 September 2022 434(17)

Plating human iPSC lines on micropatterned substrates reveals role for ITGB1 nsSNV in endoderm formation

Authors: Vickers, Alice, Tewary, Mukul, Laddach, Anna, Poletti, Martina, Salameti, Vasiliki, Fraternali, Franca, Danovi, Davide, Watt, Fiona M.

Source: In Stem Cell Reports 9 November 2021 16(11):2628-2641

Peptide–membrane interactions and biotechnology; enabling next-generation synthetic biology: general discussion

Authors: Aguilar, Mibel, Bassereau, Patricia, Bastos, Margarida, Beales, Paul, Bechinger, Burkhard, Bonev, Boyan, Brand, Izabella, Chalouhi, Edward, Clarke, Ronald J., Deplazes, Evelyne, Fraternali, Franca, Fuchs, Patrick, Hoogenboom, Bart, Lund, Reidar, Mahmoudi, Najet, Milán Rodríguez, Paula, O'Shea, Paul, Pabst, Georg, Pal, Sreetama, Rice, Amy, Sanderson, John, Seddon, John, Sengupta, Durba, Siegel, David P., Srivastava, Anand, Utterström, Johanna, Vácha, Robert, van 't Hag, Leonie, Vijayakumar, Aishwarya, Zoranić, Larisa

Source: Faraday discussions. 232:463-481

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100137225260.0x000001&indx=1&recIds=ETOCvdc_100137225260.0x000001

Theoretical and experimental comparisons of simple peptide–membrane systems; towards defining the reaction space: general discussion

Authors: Aguilar, Marie-Isabel, Al Nahas, Kareem, Barrera, Francisco N., Bassereau, Patricia, Bechinger, Burkhard, Brand, Izabella, Chattopadhyay, Amitabha, Clarke, Ronald J., DeGrado, William F., Deplazes, Evelyne, Fletcher, Marcus, Fraternali, Franca, Fuchs, Patrick, Garcia-Saez, Ana J., Gilbert, Robert, Hoogenboom, Bart W., Jarin, Zack, O'Shea, Paul, Pabst, Georg, Pal, Sreetama, Sanderson, John M., Seddon, John M., Sengupta, Durba, Siegel, David P., Srivastava, Anand, Tieleman, D. Peter, Tripathy, Madhusmita, Utterström, Johanna, Vácha, Robert, Vanni, Stefano, Voth, Gregory A.

Source: Faraday discussions. 232:149-171

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100137225240.0x000001&indx=1&recIds=ETOCvdc_100137225240.0x000001

Virus-inspired designs of antimicrobial nanocapsules

Authors: Cruz, Carlos H. B., Marzuoli, Irene, Fraternali, Franca

Source: Faraday discussions. 232:448-462

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100137225223.0x000001&indx=1&recIds=ETOCvdc_100137225223.0x000001

Nanocapsule designs for antimicrobial resistanceElectronic supplementary information (ESI) available: Additional information on the capsules; alignment of Wild Type and modified β-annulus; radius of gyration of the capsules simulated; area per lipid, component density and lipidtail order of membrane simulations (no capsules); side chains/backbone hydrogen bonds for atomistic simulation of capzip capsule; radial distribution function of capzip and β-annulus capsules amino acids around bacterial membrane lipid moieties. See DOI: 10.1039/D0NR08146A

Authors: Marzuoli, Irene, Cruz, Carlos H. B., Lorenz, Christian D., Fraternali, Franca

Source: Nanoscale. 13(23):10342-10355

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100121688849.0x000001&indx=1&recIds=ETOCvdc_100121688849.0x000001

Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide

Authors: Glass, William G., Essex, Jonathan W., Fraternali, Franca, Gebbie-Rayet, James, Marzuoli, Irene, Samways, Marley L., Biggin, Philip C., Khalid, Syma

Source: Methods in molecular biology. 2302:253-274

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN626426267&indx=1&recIds=ETOCRN626426267

Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes

Authors: Marzuoli, Irene, Fraternali, Franca

Source: Methods in molecular biology. 2208:81-100

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624733447&indx=1&recIds=ETOCRN624733447

AllohubPy: Detecting Allosteric Signals Through An Information-theoretic Approach

Authors: Carmona, Oriol Gracia ^{1, 2, 3}, Kleinjung, Jens ⁵, Anastasiou, Dimitrios ⁶, Oostenbrink, Chris ⁴, Fraternali, Franca ^{1, 2, ⁎}

Source: In Journal of Molecular Biology January 2025

Symmetry-breaking transitions in the early steps of protein self-assembly

Authors: La Rosa, Carmelo, Condorelli, Marcello, Compagnini, Giuseppe, Lolicato, Fabio, Milardi, Danilo, Do, Trang Nhu, Karttunen, Mikko, Pannuzzo, Martina, Ramamoorthy, Ayyalusamy, Fraternali, Franca, Collu, Francesca, Rezaei, Human, Strodel, Birgit, Raudino, Antonio

Source: European biophysics journal. 49(2):175-191

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100164309298.0x000001&indx=1&recIds=ETOCvdc_100164309298.0x000001

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Authors: Vigilante, Alessandra, Laddach, Anna, Moens, Nathalie, Meleckyte, Ruta, Leha, Andreas, Ghahramani, Arsham, Culley, Oliver J., Kathuria, Annie, Hurling, Chloe, Vickers, Alice, Wiseman, Erika, Tewary, Mukul, Zandstra, Peter W., Durbin, Richard, Fraternali, Franca, Stegle, Oliver, Birney, Ewan, Luscombe, Nicholas M., Danovi, Davide, Watt, Fiona M.

Source: In Cell Reports 19 February 2019 26(8):2078-2087

ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation

Authors: Monypenny, James, Milewicz, Hanna, Flores-Borja, Fabian, Weitsman, Gregory, Cheung, Anthony, Chowdhury, Ruhe, Burgoyne, Thomas, Arulappu, Appitha, Lawler, Katherine, Barber, Paul R., Vicencio, Jose M., Keppler, Melanie, Wulaningsih, Wahyu, Davidson, Sean M., Fraternali, Franca, Woodman, Natalie, Turmaine, Mark, Gillett, Cheryl, Franz, Dafne, Quezada, Sergio A., Futter, Clare E., Von Kriegsheim, Alex, Kolch, Walter, Vojnovic, Borivoj, Carlton, Jeremy G., Ng, Tony

Source: In Cell Reports 17 July 2018 24(3):630-641

Genetic variants and protein–protein interactions: a multidimensional network-centric view

Authors: Laddach, Anna, Ng, Joseph Chi-Fung, Chung, Sun Sook, Fraternali, Franca

Source: In Current Opinion in Structural Biology June 2018 50:82-90