PLUMED Tutorials: a collaborative, community-driven learning ecosystem

Authors: Tribello, Gareth A., Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Armstrong, Blake I., Arsiccio, Andrea, Aureli, Simone, Ballabio, Federico, Bernetti, Mattia, Bonati, Luigi, Brookes, Samuel G. H., Brotzakis, Z. Faidon, Capelli, Riccardo, Ceriotti, Michele, Chan, Kam-Tung, Cossio, Pilar, Dasetty, Siva, Donadio, Davide, Ensing, Bernd, Ferguson, Andrew L., Fraux, Guillaume, Gale, Julian D., Gervasio, Francesco Luigi, Giorgino, Toni, Herringer, Nicholas S. M., Hocky, Glen M., Hoff, Samuel E., Invernizzi, Michele, Languin-Cattöen, Olivier, Leone, Vanessa, Limongelli, Vittorio, Lopez-Acevedo, Olga, Marinelli, Fabrizio, Martinez, Pedro Febrer, Masetti, Matteo, Mehdi, Shams, Michaelides, Angelos, Murtada, Mhd Hussein, Parrinello, Michele, Piaggi, Pablo M., Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Pritchard, Claire, Raiteri, Paolo, Raniolo, Stefano, Rapetti, Daniele, Rizzi, Valerio, Rydzewski, Jakub, Salvalaglio, Matteo, Schran, Christoph, Seal, Aniruddha, Zadeh, Armin Shayesteh, Silva, Tomás F. D., Spiwok, Vojtěch, Stirnemann, Guillaume, Sucerquia, Daniel, Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A., White, Andrew D., Wu, Jiangbo

Subject Terms: Physics - Physics Education, Physics - Chemical Physics, Physics - Computational Physics

Access URL: http://arxiv.org/abs/2412.03595

PLUMED Tutorials: A collaborative, community-driven learning ecosystem.

Authors: Tribello, Gareth A., Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Armstrong, Blake I., Arsiccio, Andrea, Aureli, Simone, Ballabio, Federico, Bernetti, Mattia, Bonati, Luigi, Brookes, Samuel G. H., Brotzakis, Z. Faidon, Capelli, Riccardo, Ceriotti, Michele, Chan, Kam-Tung, Cossio, Pilar, Dasetty, Siva, Donadio, Davide, Ensing, Bernd, Ferguson, Andrew L.

Source: Journal of Chemical Physics; 3/7/2025, Vol. 162 Issue 9, p1-14, 14p

Subject Terms: SOFTWARE compatibility, SOFTWARE maintenance, ONLINE education, COMPUTATIONAL physics, COVID-19 pandemic

Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery

Authors: Milazzo, Ferdinando M., Chaves-Sanjuan, Antonio, Minenkova, Olga, Santapaola, Daniela, Anastasi, Anna M., Battistuzzi, Gianfranco, Chiapparino, Caterina, Rosi, Antonio, Merlo Pich, Emilio, Albertoni, Claudio, Marra, Emanuele, Luberto, Laura, Viollet, Cécile, Spagnoli, Luigi G., Riccio, Anna, Rossi, Antonio, Santoro, M. Gabriella, Ballabio, Federico, Paissoni, Cristina, Camilloni, Carlo, Bolognesi, Martino, De Santis, Rita

Source: Molecular therapy. 31(2):362-373

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100180336905.0x000001&indx=1&recIds=ETOCvdc_100180336905.0x000001

Multi-eGO : An in silico lens to look into protein aggregation kinetics at atomic resolution

Authors: Scalone, Emanuele, Broggini, Luca, Visentin, Cristina, Erba, Davide, Toplek, Fran Bačić, Peqini, Kaliroi, Pellegrino, Sara, Ricagno, Stefano, Paissoni, Cristina, Camilloni, Carlo

Source: Proceedings of the National Academy of Sciences of the United States of America, 2022 Jun . 119(26), 1-10.

Access URL: https://www.jstor.org/stable/27152822

A practical guide to the simultaneous determination of protein structure and dynamics using metainference

Authors: Löhr, Thomas, Camilloni, Carlo, Bonomi, Massimiliano, Vendruscolo, Michele

Subject Terms: Quantitative Biology - Quantitative Methods, Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/1901.08030

An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations

Authors: Capelli, Riccardo, Tiana, Guido, Camilloni, Carlo

Source: The Journal of Chemical Physics 148, 184114 (2018)

Subject Terms: Quantitative Biology - Biomolecules, Condensed Matter - Statistical Mechanics

Access URL: http://arxiv.org/abs/1802.06560

Disordered Regions Flanking the Binding Interface Modulate Affinity between CBP and NCOA

Authors: Karlsson, Elin, Schnatwinkel, Jan, Paissoni, Cristina, Andersson, Eva, Herrmann, Christian, Camilloni, Carlo, Jemth, Per

Source: In Journal of Molecular Biology 15 July 2022 434(13)

A conformational fingerprint for amyloidogenic light chains.

Authors: Paissoni, Cristina, Puri, Sarita, Broggini, Luca, Sriramoju, Manoj K., Maritan, Martina, Russo, Rosaria, Speranzini, Valentina, Ballabio, Federico, Nuvolone, Mario, Merlini, Giampaolo, Palladini, Giovanni, Hsu, Shang-Te Danny, Ricagno, Stefano, Camilloni, Carlo

Source: eLife; 3/3/2025, p1-21, 21p

Estimation of Ligand Binding Free Energy Using Multi-eGO.

Authors: Stegani, Bruno, Scalone, Emanuele, Toplek, Fran Bačić, Löhr, Thomas, Gianni, Stefano, Vendruscolo, Michele, Capelli, Riccardo, Camilloni, Carlo

Source: Journal of Chemical Information & Modeling; 1/13/2025, Vol. 65 Issue 1, p351-362, 12p

High Conformational Flexibility of the E2F1/DP1/DNA Complex

Authors: Saad, Dana, Paissoni, Cristina, Chaves-Sanjuan, Antonio, Nardini, Marco, Mantovani, Roberto, Gnesutta, Nerina, Camilloni, Carlo

Source: In Journal of Molecular Biology 3 September 2021 433(18)

Converging experimental and computational views of the knotting mechanism of a small knotted protein

Authors: Paissoni, Cristina, Puri, Sarita, Wang, Iren, Chen, Szu-Yu, Camilloni, Carlo, Hsu, Shang-Te Danny

Source: In Biophysical Journal 1 June 2021 120(11):2276-2286

Metainference: A Bayesian Inference Method for Heterogeneous Systems

Authors: Bonomi, Massimiliano, Camilloni, Carlo, Cavalli, Andrea, Vendruscolo, Michele

Subject Terms: Physics - Computational Physics, Physics - Data Analysis, Statistics and Probability, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/1509.05684

The co‐existence of cold activity and thermal stability in an Antarctic GH42 β‐galactosidase relies on its hexameric quaternary arrangement

Authors: Mangiagalli, Marco, Lapi, Michela, Maione, Serena, Orlando, Marco, Brocca, Stefania, Pesce, Alessandra, Barbiroli, Alberto, Camilloni, Carlo, Pucciarelli, Sandra, Lotti, Marina, Nardini, Marco

Source: FEBS journal. 288(2):546-565

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100115380522.0x000001&indx=1&recIds=ETOCvdc_100115380522.0x000001

A kinetic ensemble of the Alzheimer's Aβ peptide

Authors: Löhr, Thomas, Kohlhoff, Kai, Heller, Gabriella T., Camilloni, Carlo, Vendruscolo, Michele

Source: Nature computational science. 1(1):71-78

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191450196.0x000001&indx=1&recIds=ETOCvdc_100191450196.0x000001

A PDZ tandem repeat folds and unfolds via different pathways.

Authors: Pennacchietti, Valeria, di Matteo, Sara, Pagano, Livia, Toplek, Fran Bačić, Stegani, Bruno, Toto, Angelo, Toso, Julian, Puglisi, Elena, Capelli, Riccardo, Di Felice, Mariana, Malagrinò, Francesca, Camilloni, Carlo, Gianni, Stefano

Source: Protein Science: A Publication of the Protein Society; Dec2024, Vol. 33 Issue 12, p1-14, 14p

Pathogenic G6PD variants: Different clinical pictures arise from different missense mutations in the same codon.

Authors: Costa, Simonetta, Minucci, Angelo, Kumawat, Amit, De Bonis, Maria, Prontera, Giorgia, Gelsomino, Mariannita, Tana, Milena, Tiberi, Eloisa, Romano, Alberto, Ruggiero, Antonio, Mastrangelo, Stefano, Palumbo, Giuseppe, Giorgio, Valentina, Onori, Maria Elisabetta, Bolognesi, Martino, Camilloni, Carlo, Luzzatto, Lucio, Vento, Giovanni

Source: British Journal of Haematology; Nov2024, Vol. 205 Issue 5, p1985-1994, 10p

Subject Terms: GLUCOSE-6-phosphate dehydrogenase deficiency, MOLECULAR dynamics, HEMOLYTIC anemia, ENZYME deficiency, MISSENSE mutation

A missense mutation in the barley Xan-h gene encoding the Mg-chelatase subunit I leads to a viable pale green line with reduced daily transpiration rate.

Authors: Persello, Andrea, Tadini, Luca, Rotasperti, Lisa, Ballabio, Federico, Tagliani, Andrea, Torricella, Viola, Jahns, Peter, Dalal, Ahan, Moshelion, Menachem, Camilloni, Carlo, Rosignoli, Serena, Hansson, Mats, Cattivelli, Luigi, Horner, David S., Rossini, Laura, Tondelli, Alessandro, Salvi, Silvio, Pesaresi, Paolo

Source: Plant Cell Reports; Oct2024, Vol. 43 Issue 10, p1-23, 23p

Mapping the transition state for a binding reaction between ancient intrinsically disordered proteins

Authors: Karlsson, Elin, Paissoni, Cristina, Erkelens, Amanda M., Tehranizadeh, Zeinab A., Sorgenfrei, Frieda A., Andersson, Eva, Ye, Weihua, Camilloni, Carlo ^*, Jemth, Per ^*

Source: In Journal of Biological Chemistry 18 December 2020 295(51):17698-17712

Conformational Stability and Dynamics in Crystals Recapitulate Protein Behavior in Solution

Authors: Sala, Benedetta Maria, Le Marchand, Tanguy, Pintacuda, Guido, Camilloni, Carlo, Natalello, Antonino, Ricagno, Stefano

Source: In Biophysical Journal 1 September 2020 119(5):978-988

HERG stereoselective modulation by mexiletine‐derived ureas: Molecular docking study, synthesis, and biological evaluation

Authors: Milani, Gualtiero, Budriesi, Roberta, Tavazzani, Elisa, Cavalluzzi, Maria Maddalena, Mattioli, Laura Beatrice, Miniero, Daniela Valeria, Delre, Pietro, Belviso, Benny Danilo, Denegri, Marco, Cuocci, Corrado, Rotondo, Natalie Paola, De Palma, Annalisa, Gualdani, Roberta, Caliandro, Rocco, Mangiatordi, Giuseppe Felice, Kumawat, Amit, Camilloni, Carlo, Priori, Silvia, Lentini, Giovanni

Source: Archiv der Pharmazie. 356(10)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195047416.0x000001&indx=1&recIds=ETOCvdc_100195047416.0x000001