Publications of the Department (MPG.PuRe list)

Schmidt, L.; de Groot, B. L.: Identification of allosteric sites and ligand-induced modulation in the dopamine receptor through large-scale alchemical mutation scan. Chemical Science (2025)

Wilson, C. J.; Gapsys, V.; de Groot, B. L.: Improving pK_a Predictions with Reparameterized Force Fields and Free Energy Calculations. Journal of Chemical Theory and Computation 21 (8), pp. 4095 - 4106 (2025)

Amaro, R. E.; Åqvist, J.; Bahar, I.; Battistini, F.; Bellaiche, A.; Beltran, D.; Biggin, P. C.; Bonomi, M.; Bowman, G. R.; Bryce, R. A. et al.; Bussi, G.; Carloni, P.; Case, D. A.; Cavalli, A.; Chang, C.-E. A.; Cheatham, T. E.; Cheung, M. S.; Chipot, C.; Chong, L. T.; Choudhary, P.; Cisneros, G. A.; Clementi, C.; Collepardo-Guevara, R.; Coveney, P.; Covino, R.; Crawford, T. D.; Dal Peraro, M.; de Groot, B. L.; Delemotte, L.; De Vivo, M.; Essex, J. W.; Fraternali, F.; Gao, J.; Gelpí, J. L.; Gervasio, F. L.; González-Nilo, F. D.; Grubmüller, H.; Guenza, M. G.; Guzman, H. V.; Harris, S.; Head-Gordon, T.; Hernandez, R.; Hospital, A.; Huang, N.; Huang, X.; Hummer, G.; Iglesias-Fernández, J.; Jensen, J. H.; Jha, S.; Jiao, W.; Jorgensen, W. L.; Kamerlin, S. C. L.; Khalid, S.; Laughton, C.; Levitt, M.; Limongelli, V.; Lindahl, E.; Lindorff-Larsen, K.; Loverde, S.; Lundborg, M.; Luo, Y. L.; Luque, F. J.; Lynch, C. I.; MacKerell, A. D.; Magistrato, A.; Marrink, S. J.; Martin, H.; McCammon, J. A.; Merz, K.; Moliner, V.; Mulholland, A. J.; Murad, S.; Naganathan, A. N.; Nangia, S.; Noe, F.; Noy, A.; Oláh, J.; O’Mara, M. L.; Ondrechen, M. J.; Onuchic, J. N.; Onufriev, A.; Osuna, S.; Palermo, G.; Panchenko, A. R.; Pantano, S.; Parish, C.; Parrinello, M.; Perez, A.; Perez-Acle, T.; Perilla, J. R.; Pettitt, B. M.; Pietropaolo, A.; Piquemal, J.-P.; Poma, A. B.; Praprotnik, M.; Ramos, M. J.; Ren, P.; Reuter, N.; Roitberg, A.; Rosta, E.; Rovira, C.; Roux, B.; Rothlisberger, U.; Sanbonmatsu, K. Y.; Schlick, T.; Shaytan, A. K.; Simmerling, C.; Smith, J. C.; Sugita, Y.; Świderek, K.; Taiji, M.; Tao, P.; Tieleman, D. P.; Tikhonova, I. G.; Tirado-Rives, J.; Tuñón, I.; van der Kamp, M. W.; van der Spoel, D.; Velankar, S.; Voth, G. A.; Wade, R.; Warshel, A.; Welborn, V. V.; Wetmore, S. D.; Wheeler, T. J.; Wong, C. F.; Yang, L.-W.; Zacharias, M.; Orozco, M.: The need to implement FAIR principles in biomolecular simulations. Nature Methods 22, pp. 641 - 645 (2025)

Morgunova, E.; Nagy, G.; Yin, Y.; Zhu, F.; Nayak, S. P.; Xiao, T.; Sokolov, I.; Popov, A.; Laughton, C.; Grubmüller, H. et al.; Taipale, J.: Interfacial water confers transcription factors with dinucleotide specificity. Nature Structural & Molecular Biology 32, pp. 650 - 661 (2025)

Singh, S.; Gapsys, V.; Aldeghi, M.; Schaller, D.; Rangwala, A. M.; White, J. B.; Bluck, J. P.; Scheen, J.; Glass, W. G.; Guo, J. et al.; Hayat, S.; de Groot, B. L.; Volkamer, A.; Christ, C. D.; Seeliger, M. A.; Chodera, J. D.: Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding. The Journal of Physical Chemistry B 129 (11), pp. 2882 - 2902 (2025)

Blom, K.; Makarov, D. E.; Godec, A.: Hallmarks of deception in asset-exchange models. Physical Review Research 7, 013279 (2025)

Dieball, C.; Godec, A.: Perspective: Time irreversibility in systems observed at coarse resolution. The Journal of Chemical Physics 162, 090901 (2025)

Briand, E.; Kohnke, B.; Kutzner, C.; Grubmüller, H.: Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications. Journal of Chemical Theory and Computation 21 (4), pp. 1762 - 1786 (2025)

Kohnke, B.; Briand, E.; Kutzner, C.; Grubmüller, H.: Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation. Journal of Chemical Theory and Computation 21 (4), pp. 1787 - 1804 (2025)

Kutzner, C.; Miletić, V.; Palacio Rodríguez, K.; Rampp, M.; Hummer, G.; de Groot, B. L.; Grubmüller, H.: Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. Journal of Computational Chemistry 46 (5), e70059 (2025)

Dieball, C.; Mohebi Satalsari, Y.; Zuccolotto-Bernez, A. B.; Egelhaaf, S. U.; Escobedo-Sánchez, M. A.; Godec, A.: Precisely controlled colloids: a playground for path-wise non-equilibrium physics. Soft Matter 21 (11), pp. 2170 - 2181 (2025)

Blom, K.; Thiele, U.; Godec, A.: Local order controls the onset of oscillations in the nonreciprocal Ising model. Physical Review E 111 (2), 024207 (2025)

Hehlert, P.; Effertz, T.; Gu, R.-X.; Nadrowski, B.; Geurten, B. R. H.; Beutner, D.; de Groot, B. L.; Göpfert, M. C.: NOMPC ion channel hinge forms a gating spring that initiates mechanosensation. Nature Neuroscience 28, pp. 259 - 267 (2025)

Sant, V.; Matthes, D.; Mazal, H.; Antonschmidt, L.; Wieser, F.; Movellan, K. T.; Xue, K.; Nimerovsky, E.; Stampolaki, M.; Nathan, M. et al.; Riedel, D.; Becker, S.; Sandoghdar, V.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: Lipidic folding pathway of α-Synuclein via a toxic oligomer. Nature Communications 16, 760 (2025)

Tabanera-Bravo, J.; Godec, A.: Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off. Physical Review Research 7, 013020 (2025)

Hui, C.; de Vries, R.; Kopec, W.; de Groot, B. L.: Effective Polarization in Potassium Channel Simulations: Ion Conductance, Occupancy, Voltage Response, and Selectivity. bioRxiv (2025)

Wilson, C. J.; Gapsys, V.; de Groot, B. L.: Improving pKa prediction accuracy with reparametrized force fields and free energy calculations. ChemRxiv (2025)