Our scientific contributions

hexABC seeking the physical code of DNA
Federica Battistini, Miłosz Wieczór, Adam Hospital, Marco Pasi, Juan Pablo Arcón, Israel Serrano-Chacón, Alba Sala, Subhamoy Deb, Agustín García-Doñate, Matthew Burman, Elliot W. Chan, Liwei Chang, Gabriela da Rosa, Jorge R. Espinosa, Gia Linh Hoang, Kazi A. Hossain, Michał Jurkowski, Romain Poupon, Rahul Sharma, Ran Sun, Thomas C. Bishop, Paolo Carloni, Thomas E. Cheatham III, Rosana Collepardo-Guevara, Jacek Czub, Pablo D. Dans, Sarah A. Harris, Charles Laughton, Rodrigo Galindo-Murillo, John H. Maddocks, Agnes Noy, Alberto Pérez, Daiva Petkevičiūtė-Gerlach, Modesto Orozco
Nature Communications. 2026.
https://doi.org/10.1038/s41467-026-74390-5

Theoretical approaches to tracing conformational polymorphism of proteins
Miłosz Wieczór, Gerard Carol, Pablo Navarro, Adam Hospital, Modesto Orozco
Current Opinion in Structural Biology. 2026.
https://doi.org/10.1016/j.sbi.2026.103392

On free energy calculations in drug discovery
Alessia Ghidini, Eleonora Serra, Andrea Cavalli
Accounts of Chemical Research. 2025
https://doi.org/10.1021/acs.accounts.5c00465

Binding free energy calculations based on the path collective variable along a string pathway
Alessia Ghidini, Andrea Cavalli, Benoit Roux
The Journal of Physical Chemistry B. 2025
https://doi.org/10.1021/acs.jpcb.5c02258

Path-based nonequilibrium binding free energy estimation, from protein-ligand to RNA-ligand binding
Eleonora Serra, Alessia Ghidini, Riccardo Aguti, Mattia Bernetti, Sergio Decherchi, Andrea Cavalli
Journal of Chemical Information and Modelling. 2025
https://doi.org/10.1021/acs.jcim.5c00452

The need to implement FAIR principles in biomolecular simulations
Rommie E. Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C. Biggin, Massimiliano Bonomi, Gregory R. Bowman, Richard A. Bryce, Giovanni Bussi, Paolo Carloni, David A. Case, Andrea Cavalli, Chie-En A. Chang, Thomas E. Cheatham III, Margaret S. Cheung, Cristophe Chipot, Lillian T. Chong, Preeti Choudhary, G. Andres Cisneros, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, T. Daniel Crawford, Matteo Dal Peraro, Bert L. de Groot, Lucie Delemotte, Marco De Vivo, Jonathan W. Essex, Franca Fraternali, Jiali Gao, Josep Ll. Gelpí, Francesco L. Gervasio, Fernando D. Gonzalez-Nilo, Helmut Grubmüller, Marina G. Guenza, Horacio V. Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H. Jensen, Shantenu Jha, Wanting Jiao, William L. Jorgensen, Shina C. L. Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kersten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun L. Luo, F. Javier Luque, Charlotte I. Lynch, Alexander D. MacKerell, Alessandra Magistrato, Siewert J. Marrink, Hugh Martin, J. Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian J. Mulholland, Sohail Murad, Athi N. Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan L. O’Mara, Mary Jo Ondrechen, José N. Onuchic, Alexey Onufriev, Silvia Osuna, Giulia Palermo, Anna R. Panchenko, Sergio Pantano, CArol Parish, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R. Perilla, B. Montgomery Pettitt, Adriana Pietropalo, Jean-Philip Piquemal, Adolfo B. Poma, Matej Praprotnik, Maria J. Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Rothlisberger, Karissa Y. Sanbonmatsu, Tamar Schlick , Alexey K. Shaytan, Carlos Simmerling, Jeremy C. Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, D. Peter Tieleman, Irina G. Tikhonova, Julian Tirado-Rives, Iñaki Tuñón, Marc W. van der Kamp, David van der Spoel, Sameer Velankar, Gregory A. Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey D. Wetmore, Travis J. Wheeler, Chung F. Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco
Nature Methods. 2025
https://doi.org/10.1038/s41592-025-02635-0

Nonequilibrium binding free energy simulations: minimizing dissipation
Eleonora Serra, Alessia Ghidini, Sergio Decherchi, Andrea Cavalli
Journal of Chemical Theory and Computation. 2025
https://doi.org/10.1021/acs.jctc.4c01453

MD-DATA: the legacy of the ABC Consortium
Adam Hospital, Modesto Orozco
Biophysical Reviews. 2024
https://doi.org/10.1007/s12551-024-01197-3

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort
Daniel Beltrán, Adam Hospital, Josep Lluís Gelpí, Modesto Orozco
Nucleic Acids Research. 2024
https://doi.org/10.1093/nar/gkad991