THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method

‘Improved parameters for the Martini coarse-grained protein force field’

de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schäfer, L. V., Periole, X., Tieleman, D. P., & Marrink, S. J. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct300646g · Cited by 1,486 · see citing works

The Protein Folding Problem

Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163 · see citing works

Extreme disorder in an ultrahigh-affinity protein complex

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Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3008099 · Cited by 343 · see citing works

Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver

Miao, L., Lin, J., Huang, Y., Li, L., Delcassian, D., Ge, Y., Shi, Y., & Anderson, D. G. (2020) · Nature Communications · doi:10.1038/s41467-020-16248-y · Cited by 343 · see citing works

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Mobley, D. L., Chodera, J. D., & Dill, K. A. (2006) · The Journal of Chemical Physics · doi:10.1063/1.2221683 · Cited by 316 · see citing works

The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data

Kollman, P., Dixon, R., Cornell, W., Fox, T., Chipot, C., & Pohorille, A. (1997) · Computer Simulation of Biomolecular Systems · doi:10.1007/978-94-017-1120-3_2 · Cited by 242 · see citing works

Molecular driving forces determining potassium channel slow inactivation

Cordero-Morales, J. F., Jogini, V., Lewis, A., Vásquez, V., Cortes, D. M., Roux, B., & Perozo, E. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1309 · Cited by 236 · see citing works

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Cournia, Z., Allen, T. W., Andricioaei, I., Antonny, B., Baum, D., Brannigan, G., Buchete, N.-V., Deckman, J. T., Delemotte, L., del Val, C., et al. (2015) · The Journal of Membrane Biology · doi:10.1007/s00232-015-9802-0 · Cited by 235 · see citing works

Using AMBER18 for Relative Free Energy Calculations

Song, L. F., Lee, T.-S., Zhu, C., York, D. M., & Merz, K. M. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00105 · Cited by 234 · see citing works

A gate in the selectivity filter of potassium channels

Bernèche, S., & Roux, B. (2005) · Structure · doi:10.1016/j.str.2004.12.019 · Cited by 214 · see citing works

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

Tribello, G. A., Ceriotti, M., & Parrinello, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201152109 · Cited by 202 · see citing works

Computational prediction of protein–protein binding affinities

Siebenmorgen, T., & Zacharias, M. (2020) · WIREs Computational Molecular Science · doi:10.1002/wcms.1448 · Cited by 184 · see citing works

Calcium ions in aqueous solutions: Accurate force field description aided by <i>ab initio</i> molecular dynamics and neutron scattering

Martinek, T., Duboué-Dijon, E., Timr, Š., Mason, P. E., Baxová, K., Fischer, H. E., Schmidt, B., Pluhařová, E., & Jungwirth, P. (2018) · The Journal of Chemical Physics · doi:10.1063/1.5006779 · Cited by 114 · see citing works

Collective action of water molecules in zeolite dealumination

Nielsen, M., Hafreager, A., Brogaard, R. Y., De Wispelaere, K., Falsig, H., Beato, P., Van Speybroeck, V., & Svelle, S. (2019) · Catalysis Science &amp; Technology · doi:10.1039/c9cy00624a · Cited by 76 · see citing works

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

Chu, X., Gan, L., Wang, E., & Wang, J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1220699110 · Cited by 62 · see citing works

How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study

Cheng, Y., Zhang, Y., & McCammon, J. A. (2006) · Protein Science · doi:10.1110/ps.051852306 · Cited by 62 · see citing works

Molecular Dynamics of Ion Hydration in the Presence of Small Carboxylated Molecules and Implications for Calcification

Hamm, L. M., Wallace, A. F., & Dove, P. M. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp9108893 · Cited by 61 · see citing works

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations

Periole, X. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00344 · Cited by 58 · see citing works

Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression

Stecher, T., Bernstein, N., & Csányi, G. (2014) · Journal of Chemical Theory and Computation · doi:10.1021/ct500438v · Cited by 56 · see citing works

Kinetic pathways of water exchange in the first hydration shell of magnesium

Schwierz, N. (2020) · The Journal of Chemical Physics · doi:10.1063/1.5144258 · Cited by 52 · see citing works

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Prinz, J.-H., Chodera, J. D., Pande, V. S., Swope, W. C., Smith, J. C., & Noé, F. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3592153 · Cited by 52 · see citing works

Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome

Allnér, O., & Nilsson, L. (2011) · RNA · doi:10.1261/rna.029231.111 · Cited by 50 · see citing works

Investigation of the role of polysaccharide in the dolomite growth at low temperature by using atomistic simulations

Shen, Z., Szlufarska, I., Brown, P. E., & Xu, H. (2015) · Langmuir · doi:10.1021/acs.langmuir.5b02025 · Cited by 31 · see citing works

Insight into the Interaction of Furfural with Metallic Surfaces in the Electrochemical Hydrogenation Process

Lenk, T., Rabet, S., Sprick, M., Raabe, G., & Schröder, U. (2023) · ChemPhysChem · doi:10.1002/cphc.202200614 · Cited by 26 · see citing works

Reactive force fields for aqueous and interfacial magnesium carbonate formation

Zare, S., & Qomi, M. J. A. (2021) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp02627e · Cited by 24 · see citing works

Charge Effects on the Fibril-Forming Peptide KTVIIE: A Two-Dimensional Replica Exchange Simulation Study

Jeon, J., & Shell, M. S. (2012) · Biophysical Journal · doi:10.1016/j.bpj.2012.03.019 · Cited by 16 · see citing works

Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT

Ohnuki, J., Jaunet-Lahary, T., Yamashita, A., & Okazaki, K.-I. (2024) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.3c03052 · Cited by 14 · see citing works

EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery

Wijeratne, H. R. S., Runnebohm, A. M., Barron, M. P., Hampton, A. J., Li, R., Peck Justice, S. A., Lenceski, S. H., Rooney, J. D., Smith-Kinnaman, W. R., Chang, G. S., et al. (2026) · doi:10.64898/2026.01.26.701775 · Cited by 1 · see citing works