Integrating cellular and molecular structures and dynamics into whole-cell models

Highly accurate protein structure prediction with AlphaFold

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works

Martini 3: A general purpose force field for coarse-grained molecular dynamics

Souza, P. C. T., Alessandri, R., Barnoud, J., Thallmair, S., Faustino, I., Grünewald, F., Patmanidis, I., Abdizadeh, H., Bruininks, B. M. H., Wassenaar, T. A., et al. (2021) · Nature Methods · doi:10.1038/s41592-021-01098-3 · Cited by 1,551 · see citing works

A Whole-Cell Computational Model Predicts Phenotype from Genotype

Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I., & Covert, M. W. (2012) · Cell · doi:10.1016/j.cell.2012.05.044 · Cited by 1,300 · see citing works

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

Chang, A., Jeske, L., Ulbrich, S., Hofmann, J., Koblitz, J., Schomburg, I., Neumann-Schaal, M., Jahn, D., & Schomburg, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1025 · Cited by 789 · see citing works

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

Park, J. O., Rubin, S. A., Xu, Y.-F., Amador-Noguez, D., Fan, J., Shlomi, T., & Rabinowitz, J. D. (2016) · Nature Chemical Biology · doi:10.1038/nchembio.2077 · Cited by 453 · see citing works

Impact of genome reduction on bacterial metabolism and its regulation

Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.-H., Wodke, J. A. H., Güell, M., Martínez, S., Bourgeois, R., et al. (2009) · Science · doi:10.1126/science.1177263 · Cited by 327 · see citing works

‘MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope’

Schmidt, R., Weihs, T., Wurm, C. A., Jansen, I., Rehman, J., Sahl, S. J., & Hell, S. W. (2021) · Nature Communications · doi:10.1038/s41467-021-21652-z · Cited by 306 · see citing works

In-cell architecture of an actively transcribing-translating expressome

O’Reilly, F. J., Xue, L., Graziadei, A., Sinn, L., Lenz, S., Tegunov, D., Blötz, C., Singh, N., Hagen, W. J. H., Cramer, P., et al. (2020) · Science · doi:10.1126/science.abb3758 · Cited by 284 · see citing works

Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistry

Goldberg, R. N., Tewari, Y. B., & Bhat, T. N. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth314 · Cited by 191 · see citing works

Essential metabolism for a minimal cell

Breuer, M., Earnest, E. E., Merryman, C., Wise, K. S., Sun, L., Lynott, M. R., Hutchison, C. A., Smith, H. O., Lapek, J. D., Gonzalez, D. J., et al. (2019) · eLife · doi:10.7554/elife.36842 · Cited by 190 · see citing works

Fundamental behaviors emerge from simulations of a living minimal cell

Thornburg, Z. R., Bianchi, D. M., Brier, T. A., Gilbert, B. R., Earnest, E. E., Melo, M. C. R., Safronova, N., Sáenz, J. P., Cook, A. T., Wise, K. S., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.025 · Cited by 165 · see citing works

The structure and function of the gram-positive bacterial RNA degradosome

Cho, K. H. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00154 · Cited by 48 · see citing works

‘Integrating experiments, theory and simulations into whole-cell models’

Luthey-Schulten, Z. (2021) · Nature Methods · doi:10.1038/s41592-021-01150-2 · Cited by 39 · see citing works

‘Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps’

Gilbert, B. R., Thornburg, Z. R., Lam, V., Rashid, F.-Z. M., Glass, J. I., Villa, E., Dame, R. T., & Luthey-Schulten, Z. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.644133 · Cited by 30 · see citing works

Bacterial initiators form dynamic filaments on single-stranded DNA monomer by monomer

Cheng, H.-M., Gröger, P., Hartmann, A., & Schlierf, M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1284 · Cited by 20 · see citing works

Genetic requirements for cell division in a genomically minimal cell

Pelletier, J. F., Sun, L., Wise, K. S., Assad-Garcia, N., Karas, B. J., Deerinck, T. J., Ellisman, M. H., Mershin, A., Gershenfeld, N., Chuang, R.-Y., et al. (2020) · bioRxiv / Cell · doi:10.1101/2020.10.07.326892

Molecular dynamics simulation of an entire cell

Stevens, J. A., Grünewald, F., van Tilburg, P. A. M., König, M., Gilbert, B. R., Brier, T. A., Thornburg, Z. R., Luthey-Schulten, Z., & Marrink, S. J. (2023) · Frontiers in Chemistry · doi:10.3389/fchem.2023.1106495 · Cited by 156 · see citing works

Bringing the genetically minimal cell to life on a computer in 4D

Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44 · see citing works

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Weigle, A. T., Feng, J.-Y., & Shukla, D. (2022) · Physical Chemistry, Chemical Physics - PCCP · doi:10.1039/d2cp02883b · Cited by 20 · see citing works

Dynamics of chromosome organization in a minimal bacterial cell

Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19 · see citing works

Modeling membranes in situ

Brown, C. M., & Marrink, ‪. J. (2024) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102837 · Cited by 20 · see citing works

Molecular Dynamics Simulations of Biological Membranes and Membrane-Associated Phenomena Across Scales

Trebesch, N., Hasdemir, H. S., Chen, T.-L., Wen, P.-C., & Tajkhorshid, E. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103071 · Cited by 14 · see citing works

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics

Brueckner, A. C., Shields, B., Kirubakaran, P., Suponya, A., Panda, M., Posy, S., Johnson, S. R., & Lakkaraju, S. K. (2024) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-024-00564-2 · Cited by 10 · see citing works

Uncovering dissipation from coarse observables: A case study of a random walk with unobserved internal states.

Igoshin, O., Kolomeisky, A., & Makarov, D. (2025) · Journal of Chemical Physics · doi:10.1063/5.0247331 · Cited by 8

EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations

Giulini, M., Fiorentini, R., Tubiana, L., Potestio, R., & Menichetti, R. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c00490 · Cited by 7 · see citing works

Whole-cell particle-based digital twin simulations from 4D lattice light-sheet microscopy data

Arkfeld, E., Wang, Z.-C., Hakozaki, H., & Schöneberg, J. (2025) · bioRxiv · doi:10.1101/2025.04.09.647865 · Cited by 2

Biomolecular condensates, emergent properties, and the mesoscale concept gap

Schmit, J. D. (2026) · Frontiers in Biophysics · doi:10.3389/frbis.2026.1927727 · Cited by 1 · see citing works

Spatially resolved reaction–diffusion modeling reveals effects of intracellular spatial heterogeneity on yeast galactose network dynamics

WU, T., Spindler, M.-C., Apsley, A. T., Earnest, E., Thornburg, Z. R., Mahamid, J., & Luthey-Schulten, Z. A. (2026) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1014811

Spatiotemporal 4D Whole-cell Modeling of a Minimal Autotroph Reveals Central Carbon Metabolism Regulated Locally by Protein Megacomplexes via Post-translational ModiBications under Light Disturbance

Johnson, C. G. M., Chan, A. N., Rozum, J. C., George, A., Parvate, A. D., Kim, D. N., Feng, S., Bohutskyi, P., Johnson, Z., Sadler, N. C., et al. (2026) · bioRxiv · doi:10.64898/2026.01.21.700212 · Cited by 1

Network structures and parameters in multiscale modeling in ErbB signaling networks.

Shinobu, A., Nagasato-Ichikawa, A., & Okada, M. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102603 · Cited by 1 · see citing works

Back and forth modeling through biological scales.

Pantano, S. (2022) · Biochemical and Biophysical Research Communications - BBRC · doi:10.1016/j.bbrc.2022.09.037 · Cited by 1 · see citing works

Computational Modeling of Energy-Dependent Radiation-Induced Cellular Damage using an Enhanced Linear–Quadratic Framework for Radiology Optimization

Yusuf, M. A., Usman, & Ahile, J. A. (2026) · Nigerian Journal of Theoretical and Environmental Physics · doi:10.62292/njtep.v4i3.2026.160

The evolution of standards in systems biology: From metabolic and multi-scale to whole-cell models

Eltzner, D., Morschel, L., & Dräger, A. (2026) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2026.100604

Defining reversible binding rates in 1D systems dependent on diffusion, density, and excluded volume

Sang, M.-K., & Johnson, M. E. (2026) · bioRxiv · doi:10.64898/2026.06.18.733157

Transforming macromolecular structures into simulations of self-assembly with ioNERDSSPreprint

Ying, Y.-M., Sang, M.-K., Au, G., Chhibber, S., Du, Y.-F., Fischer, J. A., Foley, S. L., Guo, S., Herzog-Pohl, I., Liu, Z., et al. (2026) · bioRxiv · doi:10.64898/2026.01.27.702082