The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists

Network biology: understanding the cell's functional organization

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The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media

Minton, A. P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.r100005200 · Cited by 1,474 · see citing works

The origin and evolution of cell types

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Native mass spectrometry: a bridge between interactomics and structural biology

Heck, A. J. R. (2008) · Nature Methods · doi:10.1038/nmeth.1265 · Cited by 766 · see citing works

Eukaryotic DNA Polymerases

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Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes

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A Protein Interaction Network Links GIT1, an Enhancer of Huntingtin Aggregation, to Huntington's Disease

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Cell-cell communication: New insights and clinical implications

Su, J., Song, Y., Zhu, Z., Huang, X., Fan, J., Qiao, J., & Mao, F. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01888-z · Cited by 433 · see citing works

Interrogating viral capsid assembly with ion mobility–mass spectrometry

Uetrecht, C., Barbu, I. M., Shoemaker, G. K., van Duijn, E., & Heck, A. J. R. (2011) · Nature Chemistry · doi:10.1038/nchem.947 · Cited by 267 · see citing works

Docking, scoring, and affinity prediction in CAPRI

Lensink, M. F., & Wodak, S. J. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24428 · Cited by 249 · see citing works

Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition

Lensink, M. F., Velankar, S., & Wodak, S. J. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25215 · Cited by 222 · see citing works

Integrating diverse data for structure determination of macromolecular assemblies

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Translating the genome in time and space: Specialized ribosomes, RNA regulons, and RNA-binding proteins

Shi, Z., & Barna, M. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100814-125346 · Cited by 205 · see citing works

Mass spectrometry supported determination of protein complex structure

Walzthoeni, T., Leitner, A., Stengel, F., & Aebersold, R. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.02.008 · Cited by 146 · see citing works

Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions

Schmid, E. W., & Walter, J. C. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.034 · Cited by 120 · see citing works

Interpretation of cancer mutations using a multiscale map of protein systems

Zheng, F., Kelly, M. R., Ramms, D. J., Heintschel, M. L., Tao, K., Tutuncuoglu, B., Lee, J. J., Ono, K., Foussard, H., Chen, M., et al. (2021) · Science · doi:10.1126/science.abf3067 · Cited by 81 · see citing works

Integrative structure modeling of macromolecular assemblies from proteomics data

Lasker, K., Phillips, J. L., Russel, D., Velázquez-Muriel, J., Schneidman-Duhovny, D., Tjioe, E., Webb, B., Schlessinger, A., & Sali, A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r110.000067 · Cited by 71 · see citing works

Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry

Vimer, S., Ben-Nissan, G., Morgenstern, D., Kumar-Deshmukh, F., Polkinghorn, C., Quintyn, R. S., Vasil’ev, Y. V., Beckman, J. S., Elad, N., Wysocki, V. H., et al. (2020) · ACS Central Science · doi:10.1021/acscentsci.0c00080 · Cited by 63 · see citing works

Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes

Mousson, F., Kolkman, A., Pijnappel, W. W. M. P., Timmers, H. T. M., & Heck, A. J. R. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700306-mcp200 · Cited by 67 · see citing works

Hydrogen-deuterium exchange as a probe of folding and assembly in viral capsids11Edited by C. R. Matthews

Tuma, R., Coward, L. U., Kirk, M. C., Barnes, S., & Prevelige, P. E. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4383 · Cited by 53 · see citing works

Identification of Subunit−Subunit Interactions in Bacteriophage P22 Procapsids by Chemical Cross-linking and Mass Spectrometry

Kang, S., Hawkridge, A. M., Johnson, K. L., Muddiman, D. C., & Prevelige, P. E. (2006) · Journal of Proteome Research · doi:10.1021/pr050356f · Cited by 52 · see citing works

Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes

Suderman, R., & Deeds, E. J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003278 · Cited by 52 · see citing works

Stochastic machines as a colocalization mechanism for scaffold protein function

Xue, B., Romero, P. R., Noutsou, M., Maurice, M. M., Rüdiger, S. G. D., William, A. M., Mizianty, M. J., Kurgan, L., Uversky, V. N., & Dunker, A. K. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.04.006 · Cited by 47 · see citing works

Utilizing Microchip Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry

Black, W. A., Stocks, B. B., Mellors, J. S., Engen, J. R., & Ramsey, J. M. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b01179 · Cited by 35 · see citing works

A Docking Model Based on Mass Spectrometric and Biochemical Data Describes Phage Packaging Motor Incorporation

Fu, C.-Y., Uetrecht, C., Kang, S., Morais, M. C., Heck, A. J. R., Walter, M. R., & Prevelige, P. E. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900625-mcp200 · Cited by 33 · see citing works

Using statistical methods to model the fine-tuning of molecular machines and systems

Thorvaldsen, S., & Hössjer, O. (2020) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2020.110352 · Cited by 15 · see citing works

The Return of the God Hypothesis

Meyer, S. C., & Institute for Interdisciplinary Research (1999) · Journal of Interdisciplinary Studies · doi:10.5840/jis1999111/21 · Cited by 16 · see citing works

Méthodes d'analyse comparée des pangénomes procaryotes : explorer la diversité génomique inter-espèces pour une meilleure compréhension du métabolisme

Arnoux, J. (2026) · Thèse de doctorat, Université Paris-Saclay / PPanGGOLiN · doi:10.70675/eee354d9zf63dz48ebz9444zd1809f8fb74d

Untitled work

Zhumadilova, K. (2026) · VTechWorks (Virginia Tech)