P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation

‘GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers’

Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190

Computer Simulation of Liquids

Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945

Molecular interaction and inhibition of SARS-CoV-2 binding to the ACE2 receptor

Yang, J., Petitjean, S. J. L., Koehler, M., Zhang, Q., Dumitru, A. C., Chen, W., Derclaye, S., Vincent, S. P., Soumillion, P., & Alsteens, D. (2020) · Nature Communications · doi:10.1038/s41467-020-18319-6 · Cited by 615

Molecular origins of fluorocarbon hydrophobicity

Dalvi, V. H., & Rossky, P. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0915169107 · Cited by 421

Accurate calculation of the absolute free energy of binding for drug molecules

Aldeghi, M., Heifetz, A., Bodkin, M. J., Knapp, S., & Biggin, P. C. (2016) · Chemical Science · doi:10.1039/c5sc02678d · Cited by 347

Random heteropolymers preserve protein function in foreign environments

Panganiban, B., Qiao, B., Jiang, T., DelRe, C., Obadia, M. M., Nguyen, T. D., Smith, A. A. A., Hall, A., Sit, I., Crosby, M. G., et al. (2018) · Science · doi:10.1126/science.aao0335 · Cited by 294

Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators

Song, G., Yang, D., Wang, Y., de Graaf, C., Zhou, Q., Jiang, S., Liu, K., Cai, X., Dai, A., Lin, G., et al. (2017) · Nature · doi:10.1038/nature22378 · Cited by 241

AlphaFold2: A Role for Disordered Protein/Region Prediction?

Wilson, C. J., Choy, W.-Y., & Karttunen, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094591 · Cited by 173

The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase

Wongnate, T., Sliwa, D., Ginovska, B., Smith, D., Wolf, M. W., Lehnert, N., Raugei, S., & Ragsdale, S. W. (2016) · Science · doi:10.1126/science.aaf0616 · Cited by 170

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

Heybrock, S., Kanerva, K., Meng, Y., Ing, C., Liang, A., Xiong, Z.-J., Weng, X., Ah Kim, Y., Collins, R., Trimble, W., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11425-0 · Cited by 164

Structural insights into multiplexed pharmacological actions of tirzepatide and peptide 20 at the GIP, GLP-1 or glucagon receptors

Zhao, F., Zhou, Q., Cong, Z., Hang, K., Zou, X., Zhang, C., Chen, Y., Dai, A., Liang, A., Ming, Q., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28683-0 · Cited by 149

A molecular mechanism for transthyretin amyloidogenesis

Yee, A. W., Aldeghi, M., Blakeley, M. P., Ostermann, A., Mas, P. J., Moulin, M., de Sanctis, D., Bowler, M. W., Mueller-Dieckmann, C., Mitchell, E. P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08609-z · Cited by 139

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

Histone acetylation regulates chromatin accessibility: Role of H4K16 in inter-nucleosome interaction

Zhang, R., Erler, J., & Langowski, J. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2016.11.015 · Cited by 142

A mechanism for lipid binding to apoE and the role of intrinsically disordered regions coupled to domain-domain interactions

Frieden, C., Wang, H., & Ho, C. M. W. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1705080114 · Cited by 134

Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex

Gruszczyk, J., Grandvuillemin, L., Lai-Kee-Him, J., Paloni, M., Savva, C. G., Germain, P., Grimaldi, M., Boulahtouf, A., Kwong, H.-S., Bous, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34773-w · Cited by 137

Structural conservation of antibiotic interaction with ribosomes

Paternoga, H., Crowe-McAuliffe, C., Bock, L. V., Koller, T. O., Morici, M., Beckert, B., Myasnikov, A. G., Grubmüller, H., Nováček, J., & Wilson, D. N. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01047-y · Cited by 94

SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential

Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.03.024 · Cited by 84

How multisite phosphorylation impacts the conformations of intrinsically disordered proteins

Jin, F., & Gräter, F. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1008939 · Cited by 77

Molecular basis of proton sensing by G protein-coupled receptors

Howard, M. K., Hoppe, N., Huang, X.-P., Mitrovic, D., Billesbølle, C. B., Macdonald, C. B., Mehrotra, E., Rockefeller Grimes, P., Trinidad, D. D., Delemotte, L., et al. (2025) · Cell · doi:10.1016/j.cell.2024.11.036 · Cited by 77

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

Calmettes, C., Ing, C., Buckwalter, C. M., El Bakkouri, M., Chieh-Lin Lai, C., Pogoutse, A., Gray-Owen, S. D., Pomès, R., & Moraes, T. F. (2015) · Nature Communications · doi:10.1038/ncomms8996 · Cited by 71

Branched peptides integrate into self-assembled nanostructures and enhance biomechanics of peptidic hydrogels

Pugliese, R., Fontana, F., Marchini, A., & Gelain, F. (2018) · Acta Biomaterialia · doi:10.1016/j.actbio.2017.11.026 · Cited by 65

CaMKII binds both substrates and activators at the active site

Özden, C., Sloutsky, R., Mitsugi, T., Santos, N., Agnello, E., Gaubitz, C., Foster, J., Lapinskas, E., Esposito, E. A., Saneyoshi, T., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111064 · Cited by 61

A kinetic ensemble of the Alzheimer’s Aβ peptide

Löhr, T., Kohlhoff, K., Heller, G. T., Camilloni, C., & Vendruscolo, M. (2021) · Nature Computational Science · doi:10.1038/s43588-020-00003-w · Cited by 57

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

Metastable Prepores in Tension-Free Lipid Bilayers

Ting, C. L., Awasthi, N., Müller, M., & Hub, J. S. (2018) · Physical Review Letters · doi:10.1103/physrevlett.120.128103 · Cited by 54

Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms

Stuchell-Brereton, M. D., Zimmerman, M. I., Miller, J. J., Mallimadugula, U. L., Incicco, J. J., Roy, D., Smith, L. G., Cubuk, J., Baban, B., DeKoster, G. T., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215371120 · Cited by 48

Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds

Kwong, H.-S., Paloni, M., Grandvuillemin, L., Sirounian, S., Ancelin, A., Lai-Kee-Him, J., Grimaldi, M., Carivenc, C., Lancey, C., Ragan, T. J., et al. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2023.168411 · Cited by 40

Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields

Gopal, S. M., Wingbermühle, S., Schnatwinkel, J., Juber, S., Herrmann, C., & Schäfer, L. V. (2021) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c08702 · Cited by 37

‘Assembly and analysis of cell-scale membrane envelopes’

Vermaas, J. V., Mayne, C. G., Shinn, E., & Tajkhorshid, E. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01050 · Cited by 30

Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning

Mitrovic, D., McComas, S. E., Alleva, C., Bonaccorsi, M., Drew, D., & Delemotte, L. (2023) · eLife · doi:10.7554/elife.84805 · Cited by 31

Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain

Chi, G., Liang, Q., Sridhar, A., Cowgill, J. B., Sader, K., Radjainia, M., Qian, P., Castro-Hartmann, P., Venkaya, S., Singh, N. K., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29594-w · Cited by 28

GCN5–ERK lactylation–phosphorylation loop amplifies lactate-driven cancer progression

Huang, B., Jin, M., Cui, G., Wang, Z., Wang, F., Chen, M., Zhu, L., Li, Y., Yang, X., Li, R., et al. (2026) · Nature Chemical Biology · doi:10.1038/s41589-025-02107-8 · Cited by 24

Characterization of Protein Flexibility Using Small-Angle X-Ray Scattering and Amplified Collective Motion Simulations

Wen, B., Peng, J., Zuo, X., Gong, Q., & Zhang, Z. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.07.005 · Cited by 20

Tld1 is a regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation

Speer, N. O., Braun, R. J., Reynolds, E. G., Brudnicka, A., Swanson, J. M. J., & Henne, W. M. (2024) · Journal of Cell Biology · doi:10.1083/jcb.202303026 · Cited by 19

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

Pfoh, R., Subramanian, A. S., Huang, J., Little, D. J., Forman, A., DiFrancesco, B. R., Balouchestani-Asli, N., Kitova, E. N., Klassen, J. S., Pomès, R., et al. (2022) · PLOS Pathogens · doi:10.1371/journal.ppat.1010750 · Cited by 17

Substrate transport and drug interaction of human thiamine transporters SLC19A2/A3

Li, P., Zhu, Z., Wang, Y., Zhang, X., Yang, C., Zhu, Y., Zhou, Z., Chao, Y., Long, Y., Gao, Y., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-55359-8 · Cited by 17

Biomimetic supramolecular protein matrix restores structure and properties of human dental enamel

Hasan, A., Chuvilin, A., Van Teijlingen, A., Rouco, H., Parmenter, C., Venturi, F., Fay, M., Greco, G., Pugno, N. M., Ruben, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64982-y · Cited by 15

Rational Design by Structural Biology of Industrializable, Long-Acting Antihyperglycemic GLP-1 Receptor Agonists

Sun, L., Zheng, Z.-M., Shao, C.-S., Zhang, Z.-Y., Li, M.-W., Wang, L., Wang, H., Zhao, G.-H., & Wang, P. (2022) · Pharmaceuticals · doi:10.3390/ph15060740 · Cited by 17

Insights into the low‐temperature adaptation of an enzyme as studied through ancestral sequence reconstruction

Cui, S., Dasgupta, S., Yagi, S., Kimura, M., Furukawa, R., Tagami, S., & Akanuma, S. (2025) · Protein Science · doi:10.1002/pro.70071 · Cited by 12

Multi- e GO: Model Improvements toward the Study of Complex Self-Assembly Processes

Bačić Toplek, F., Scalone, E., Stegani, B., Paissoni, C., Capelli, R., & Camilloni, C. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01182 · Cited by 12

Barnacle cement protein as an efficient bioinspired corrosion inhibitor

Bui, M. H., Hiew, S. H., Salim, T., Saw, W. G., Webster, R. D., Grüber, G., Mu, Y., & Miserez, A. (2024) · Communications Materials · doi:10.1038/s43246-024-00445-z · Cited by 12

Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B

(2022) · doi:10.1371/journal.pcbi.1010074 · Cited by 12

Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers

van der Sleen, L., Stevens, J. A., Marrink, S. J., Poolman, B., & Tych, K. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114110 · 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

Interfacial water confers transcription factors with dinucleotide specificity

(2025) · doi:10.1038/s41594-024-01449-6 · Cited by 11

An NADH-controlled gatekeeper of ATP synthase

Schildhauer, F., Ryl, P. S. J., Lauer, S. M., Lenz, S., Barlas, A. B., Ouzounidis, V. R., Jeffrey, K., Marcu, D.-C., O’Reilly, F. J., Graziadei, A., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.06.007 · Cited by 11

Exploring the influence of pore shape on conductance and permeation

Seiferth, D., & Biggin, P. C. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.07.010 · Cited by 9

Reversible Control of Native GluN2B-Containing NMDA Receptors with Visible Light

Geoffroy, C., Berraud-Pache, R., Chéron, N., McCort-Tranchepain, I., Doria, J., Paoletti, P., & Mony, L. (2024) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.4c00247 · Cited by 9

Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2

Chávez-García, C., Hénin, J., & Karttunen, M. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01354 · Cited by 8

Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions

Becker, R. A., & Hub, J. S. (2023) · Communications Biology · doi:10.1038/s42003-023-04751-z · Cited by 7

Substrate recruitment via eIF2γ enhances catalytic efficiency of a holophosphatase that terminates the integrated stress response

Yan, Y., Shetty, M., Harding, H. P., George, G., Zyryanova, A., Labbé, K., Mafi, A., Hao, Q., Sidrauski, C., & Ron, D. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2320013121 · Cited by 7

Conformations of a highly expressed Z19 α-zein studied with AlphaFold2 and MD simulations

(2024) · doi:10.1371/journal.pone.0293786 · Cited by 7

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

Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin

Westerlund, A. M., Sridhar, A., Dahl, L., Andersson, A., Bodnar, A.-Y., & Delemotte, L. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1010583 · Cited by 6

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints

Michaelis, M., Cupellini, L., Mensch, C., Perry, C. C., Delle Piane, M., & Colombi Ciacchi, L. (2023) · Chemical Science · doi:10.1039/d3sc02202a · Cited by 6

Alanine scanning of the yeast killer toxin K2 reveals key residues for activity, gain-of-function variants, and supports prediction of precursor processing and 3D structure

(2025) · doi:10.1016/j.yjsbx.2025.100142 · Cited by 4

Conformational dynamics of a histidine molecular switch in a cation/proton antiporter

(2025) · doi:10.1016/j.bbabio.2025.149563 · Cited by 4

Molecular basis of prostaglandin E2 reuptake by organic anion transporter PGT

Zhu, Z., Li, Y., Xia, H., Yang, C., Zhou, Z., Chao, Y., Ba, Q., Li, D., & Qu, Q. (2025) · Nature Communications · doi:10.1038/s41467-025-67025-8 · Cited by 2

Coarse-Graining the Recognition of a Glycolipid by the C-Type Lectin Mincle Receptor

Noriega, M., Corey, R. A., Haanappel, E., Demange, P., Czaplicki, G., Atkinson, R. A., & Chavent, M. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c03242 · Cited by 2

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

(2023) · doi:10.32920/24746796 · Cited by 1

The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing

Pfoh, R., Subramanian, A. S., Huang, J., Little, D., Forman, A., DiFrancesco, B. R., Balouchestani-Asli, N., Kitova, E. N., Klassen, J. S., Pomès, R., et al. (2023) · doi:10.32920/24746796.v1