Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science von Laio, Alessandro, Gervasio, Francesco L

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Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations von Oleinikovas, Vladimiras, Saladino, Giorgio, Cossins, Benjamin P, Gervasio, Francesco L

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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations von Kuzmanic, Antonija, Bowman, Gregory R, Juarez-Jimenez, Jordi, Michel, Julien, Gervasio, Francesco L

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Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies von Evans, Rhys, Hovan, Ladislav, Tribello, Gareth A, Cossins, Benjamin P, Estarellas, Carolina, Gervasio, Francesco L

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Importance of the Force Field Choice in Capturing Functionally Relevant Dynamics in the von Willebrand Factor von Kuzmanic, Antonija, Pritchard, Ruth B, Hansen, D. Flemming, Gervasio, Francesco L

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Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells von Tsuchiya, Yugo, Zhyvoloup, Alexander, Baković, Jovana, Thomas, Naam, Yu, Bess Yi Kun, Das, Sayoni, Orengo, Christine, Newell, Clare, Ward, John, Saladino, Giorgio, Comitani, Federico, Gervasio, Francesco L, Malanchuk, Oksana M, Khoruzhenko, Antonina I, Filonenko, Valeriy, Peak-Chew, Sew Yeu, Skehel, Mark, Gout, Ivan

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Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase von Schulze, Jörg O., Saladino, Giorgio, Busschots, Katrien, Neimanis, Sonja, Süß, Evelyn, Odadzic, Dalibor, Zeuzem, Stefan, Hindie, Valerie, Herbrand, Amanda K., Lisa, María-Natalia, Alzari, Pedro M., Gervasio, Francesco L., Biondi, Ricardo M.

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Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics von Lovera, Silvia, Morando, Maria, Pucheta-Martinez, Encarna, Martinez-Torrecuadrada, Jorge L, Saladino, Giorgio, Gervasio, Francesco L

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The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers von Zanetti-Domingues, Laura C., Korovesis, Dimitrios, Needham, Sarah R., Tynan, Christopher J., Sagawa, Shiori, Roberts, Selene K., Kuzmanic, Antonija, Ortiz-Zapater, Elena, Jain, Purvi, Roovers, Rob C., Lajevardipour, Alireza, van Bergen en Henegouwen, Paul M. P., Santis, George, Clayton, Andrew H. A., Clarke, David T., Gervasio, Francesco L., Shan, Yibing, Shaw, David E., Rolfe, Daniel J., Parker, Peter J., Martin-Fernandez, Marisa L.

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Drug-resistant EGFR mutations promote lung cancer by stabilizing interfaces in ligand-free kinase-active EGFR oligomers von Iyer, R. Sumanth, Needham, Sarah R., Galdadas, Ioannis, Davis, Benjamin M., Roberts, Selene K., Man, Rico C. H., Zanetti-Domingues, Laura C., Clarke, David T., Fruhwirth, Gilbert O., Parker, Peter J., Rolfe, Daniel J., Gervasio, Francesco L., Martin-Fernandez, Marisa L.

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Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations von Kuzmanic, Antonija, Sutto, Ludovico, Saladino, Giorgio, Nebreda, Angel R, Gervasio, Francesco L, Orozco, Modesto

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Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms von Cavalli, Andrea, Spitaleri, Andrea, Saladino, Giorgio, Gervasio, Francesco L.

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Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions von Bešker, Neva, Gervasio, Francesco L.

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Defining an Optimal Metric for the Path Collective Variables von Hovan, Ladislav, Comitani, Federico, Gervasio, Francesco L

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Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained von Cucinotta, Clotilde S., Kosa, Monica, Melchiorre, Paolo, Cavalli, Andrea, Gervasio, Francesco L.

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Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer von Martin-Fernandez, Marisa L, Clarke, David T, Roberts, Selene K, Zanetti-Domingues, Laura C, Gervasio, Francesco L

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Structural basis of connexin-36 gap junction channel inhibition von Ding, Xinyue, Aureli, Simone, Vaithia, Anand, Lavriha, Pia, Schuster, Dina, Khanppnavar, Basavraj, Li, Xiaodan, Blum, Thorsten B., Picotti, Paola, Gervasio, Francesco L., Korkhov, Volodymyr M.

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The SH2 domain regulates c-Abl kinase activation by a cyclin-like mechanism and remodulation of the hinge motion von Dölker, Nicole, Górna, Maria W, Sutto, Ludovico, Torralba, Antonio S, Superti-Furga, Giulio, Gervasio, Francesco L

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Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus von Muñoz, Inés G, Prieto, Jesús, Subramanian, Sunita, Coloma, Javier, Redondo, Pilar, Villate, Maider, Merino, Nekane, Marenchino, Marco, D'Abramo, Marco, Gervasio, Francesco L, Grizot, Sylvestre, Daboussi, Fayza, Smith, Julianne, Chion-Sotinel, Isabelle, Pâques, Frédéric, Duchateau, Philippe, Alibés, Andreu, Stricher, François, Serrano, Luis, Blanco, Francisco J, Montoya, Guillermo

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The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study von Bunney, Tom D., Wan, Shunzhou, Thiyagarajan, Nethaji, Sutto, Ludovico, Williams, Sarah V., Ashford, Paul, Koss, Hans, Knowles, Margaret A., Gervasio, Francesco L., Coveney, Peter V., Katan, Matilda

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