A molecular dynamics method for simulations in the canonical ensemble

Computer Simulation of Liquids

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Antidepressant drugs act by directly binding to TRKB neurotrophin receptors

Casarotto, P. C., Girych, M., Fred, S. M., Kovaleva, V., Moliner, R., Enkavi, G., Biojone, C., Cannarozzo, C., Sahu, M. P., Kaurinkoski, K., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.034 · Cited by 663

Theoretical Insights into Heterogeneous (Photo)electrochemical CO2Reduction

Xu, S., & Carter, E. A. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00481 · Cited by 652

Assessing the Accuracy of Metadynamics

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Versatile object-oriented toolkit for coarse-graining applications

Rühle, V., Junghans, C., Lukyanov, A., Kremer, K., & Andrienko, D. (2009) · Journal of Chemical Theory and Computation · doi:10.1021/ct900369w · Cited by 485

Progress and challenges in the automated construction of Markov state models for full protein systems

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Hydration of the calcium ion. An EXAFS, large-angle X-ray scattering, and molecular dynamics simulation study

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Femtosecond x-ray spectroscopy of an electrocyclic ring-opening reaction

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First-principles study of Li ion diffusion inLiFePO4

Ouyang, C., Shi, S., Wang, Z., Huang, X., & Chen, L. (2004) · Physical Review B · doi:10.1103/physrevb.69.104303 · Cited by 297

Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation

Qiao, Q., Bowman, G. R., & Huang, X. (2013) · Journal of the American Chemical Society · doi:10.1021/ja403147m · Cited by 182

Molecular Dynamics Studies of Interfacial Water at the Alumina Surface

Argyris, D., Ho, T., Cole, D. R., & Striolo, A. (2011) · The Journal of Physical Chemistry C · doi:10.1021/jp109244c · Cited by 167

Structure, Dynamics, and Spectral Diffusion of Water from First-Principles Molecular Dynamics

Bankura, A., Karmakar, A., Carnevale, V., Chandra, A., & Klein, M. L. (2014) · The Journal of Physical Chemistry C · doi:10.1021/jp506120t · Cited by 166

Lysosomal integral membrane protein-2 (LIMP-2/SCARB2) is involved in lysosomal cholesterol export

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Historical contingency and its biophysical basis in glucocorticoid receptor evolution

Harms, M. J., & Thornton, J. W. (2014) · Nature · doi:10.1038/nature13410 · Cited by 147

Ethylene Carbonate‐Free Propylene Carbonate‐Based Electrolytes with Excellent Electrochemical Compatibility for Li‐Ion Batteries through Engineering Electrolyte Solvation Structure

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Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

Granata, D., Camilloni, C., Vendruscolo, M., & Laio, A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218350110 · Cited by 143

Biophysical and Ultrastructural Characterization of Adeno-Associated Virus Capsid Uncoating and Genome Release

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A coarse-graining procedure for flexible polymer chains with bonded and nonbonded interactions

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Detailed molecular dynamics simulation of the self-diffusion of n-alkane and cis-1,4 polyisoprene oligomer melts

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Coarse-grained modeling of polystyrene in various environments by iterative Boltzmann inversion

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Structure of SARS-CoV-2 M protein in lipid nanodiscs

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Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme

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Lattice anharmonicity, phonon dispersion, and thermal conductivity of PbTe studied by the phonon quasiparticle approach

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The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD

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Nuclear quantum effects on zeolite proton hopping kinetics explored with machine learning potentials and path integral molecular dynamics

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MagiC: software package for multiscale modeling

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Dispersion of Nafion Ionomer Aggregates in 1-Propanol/Water Solutions: Effects of Ionomer Concentration, Alcohol Content, and Salt Addition

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Mapping the Substrate Recognition Pathway in Cytochrome P450

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Ion Distribution and Hydration Structure in the Stern Layer on Muscovite Surface

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Extended ensemble molecular dynamics method for constant strain rate uniaxial deformation of polymer systems

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A proteome-wide map of 20(S)-hydroxycholesterol interactors in cell membranes

Cheng, Y.-S., Zhang, T., Ma, X., Pratuangtham, S., Zhang, G. C., Ondrus, A. A., Mafi, A., Lomenick, B., Jones, J. J., & Ondrus, A. E. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00907-2 · Cited by 56

Entanglements and dynamics of polymer melts near a SWCNT

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Structural basis for host recognition and superinfection exclusion by bacteriophage T5

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Systematic coarse graining: Four lessons and a caveat from nonequilibrium statistical mechanics

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Predicting oxidation and spin states by high-dimensional neural networks: Applications to lithium manganese oxide spinels

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Simulating the fabrication of aluminium oxide tunnel junctions

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Multiscale simulation of polymer melt viscoelasticity: Expanded-ensemble Monte Carlo coupled with atomistic nonequilibrium molecular dynamics

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Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre

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Unusual terahertz-wave absorptions in δ/α-mixed-phase FAPbI3 single crystals: interfacial phonon vibration modes

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Untitled work

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Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy

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Structural mechanisms for VMAT2 inhibition by tetrabenazine

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The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations

Samsudin, F., Gan, S. K.-E., & Bond, P. J. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.12.022 · Cited by 16

A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

Newman, K. E., Tindall, S. N., Mader, S. L., Khalid, S., Thomas, G. H., & Van Der Woude, M. W. (2023) · eLife · doi:10.7554/elife.81547 · Cited by 12

Association of Both Inhibitory and Stimulatory Gα Subunits Implies Adenylyl Cyclase 5 Deactivation

van Keulen, S. C., Narzi, D., & Rothlisberger, U. (2019) · Biochemistry · doi:10.1021/acs.biochem.9b00662 · Cited by 11

The intrinsically disordered transcriptional activation domain of CIITA is functionally tuneable by single substitutions: An exception or a new paradigm?

Sreenivasan, S., Heffren, P., Suh, K., Rodnin, M. V., Kosa, E., Fenton, A. W., Ladokhin, A. S., Smith, P. E., Fontes, J. D., & Swint‐Kruse, L. (2024) · Protein Science · doi:10.1002/pro.4863 · Cited by 11

Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations

Rivel, T., Biriukov, D., Kabelka, I., & Vácha, R. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01960 · Cited by 9

Control of Golgi- V-ATPase through Sac1-dependent co-regulation of PI(4)P and cholesterol

Zhou, X., van der Stoel, M. M., Kaptan, S., Li, H., Li, S., Hölttä, M., Vihinen, H., Jokitalo, E., Thiele, C., Pietiläinen, O., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63125-7 · Cited by 6

A Coarse-Grained MARTINI Model for Mucins

Kanesalingam, T., Weiand, E., Cann, P. M., Masen, M., & Ewen, J. P. (2026) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01655 · Cited by 6

Structural mechanisms for VMAT2 inhibition by tetrabenazine

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PURA and GLUT1: Sweet partners for brain health

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Mapping structural and dynamic divergence across the MBOAT family

Ansell, T. B., Healy, M., Coupland, C. E., Sansom, M. S. P., & Siebold, C. (2024) · Structure · doi:10.1016/j.str.2024.03.014 · Cited by 4