CHARMM‐GUI: A web‐based graphical user interface for CHARMM

Computer Simulation of Liquids

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

Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite

Cerutti, G., Guo, Y., Zhou, T., Gorman, J., Lee, M., Rapp, M., Reddem, E. R., Yu, J., Bahna, F., Bimela, J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.005 · Cited by 519 · see citing works

Effects of Charge on Antibody Tissue Distribution and Pharmacokinetics

Boswell, C. A., Tesar, D. B., Mukhyala, K., Theil, F.-P., Fielder, P. J., & Khawli, L. A. (2010) · Bioconjugate Chemistry · doi:10.1021/bc100261d · Cited by 398 · see citing works

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

Muller, M. P., Jiang, T., Sun, C., Lihan, M., Pant, S., Mahinthichaichan, P., Trifan, A., & Tajkhorshid, E. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00608 · Cited by 282 · see citing works

Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site

Mazhab-Jafari, M. T., Marshall, C. B., Smith, M. J., Gasmi-Seabrook, G. M. C., Stathopulos, P. B., Inagaki, F., Kay, L. E., Neel, B. G., & Ikura, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419895112 · Cited by 220 · see citing works

Discovering highly potent antimicrobial peptides with deep generative model HydrAMP

Szymczak, P., Możejko, M., Grzegorzek, T., Jurczak, R., Bauer, M., Neubauer, D., Sikora, K., Michalski, M., Sroka, J., Setny, P., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36994-z · Cited by 231 · see citing works

Structural basis of ketamine action on human NMDA receptors

Zhang, Y., Ye, F., Zhang, T., Lv, S., Zhou, L., Du, D., Lin, H., Guo, F., Luo, C., & Zhu, S. (2021) · Nature · doi:10.1038/s41586-021-03769-9 · Cited by 218 · see citing works

Cryo-EM structure of islet amyloid polypeptide fibrils reveals similarities with amyloid-β fibrils

Röder, C., Kupreichyk, T., Gremer, L., Schäfer, L. U., Pothula, K. R., Ravelli, R. B. G., Willbold, D., Hoyer, W., & Schröder, G. F. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0442-4 · Cited by 180 · see citing works

Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides

Pandi, A., Adam, D., Zare, A., Trinh, V. T., Schaefer, S. L., Burt, M., Klabunde, B., Bobkova, E., Kushwaha, M., Foroughijabbari, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42434-9 · Cited by 173 · see citing works

A gating mechanism of pentameric ligand-gated ion channels

Calimet, N., Simoes, M., Changeux, J.-P., Karplus, M., Taly, A., & Cecchini, M. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313785110 · Cited by 150 · see citing works

CG2AT2: An enhanced fragment-based approach for serial multi-scale molecular dynamics simulations

Vickery, O. N., & Stansfeld, P. J. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00295 · Cited by 150 · see citing works

Ins and outs of AlphaFold2 transmembrane protein structure predictions

Hegedűs, T., Geisler, M., Lukács, G. L., & Farkas, B. (2022) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-04112-1 · Cited by 127 · see citing works

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136 · see citing works

Direct protein-lipid interactions shape the conformational landscape of secondary transporters

Martens, C., Shekhar, M., Borysik, A. J., Lau, A. M., Reading, E., Tajkhorshid, E., Booth, P. J., & Politis, A. (2018) · Nature Communications · doi:10.1038/s41467-018-06704-1 · Cited by 134 · see citing works

Martinize2 and Vermouth provide a unified framework for molecular topology generation

Kroon, P. C., Grünewald, F., Barnoud, J., van Tilburg, M., Brasnett, C., Souza, P. C., Wassenaar, T. A., & Marrink, S. J. (2025) · eLife · doi:10.7554/elife.90627 · Cited by 124 · see citing works

A prebiotic basis for ATP as the universal energy currency

Pinna, S., Kunz, C., Halpern, A., Harrison, S. A., Jordan, S. F., Ward, J., Werner, F., & Lane, N. (2022) · PLOS Biology · doi:10.1371/journal.pbio.3001437 · Cited by 103 · see citing works

General Theory for Multiple Input-Output Perturbations in Complex Molecular Systems. 1. Linear QSPR Electronegativity Models in Physical, Organic, and Medicinal Chemistry

Gonzalez-Diaz, H., Arrasate, S., Gomez-SanJuan, A., Sotomayor, N., Lete, E., Besada-Porto, L., & Ruso, J. (2013) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026611313140011 · Cited by 101 · see citing works

Receptor Activity-modifying Protein-directed G Protein Signaling Specificity for the Calcitonin Gene-related Peptide Family of Receptors

Weston, C., Winfield, I., Harris, M., Hodgson, R., Shah, A., Dowell, S. J., Mobarec, J. C., Woodlock, D. A., Reynolds, C. A., Poyner, D. R., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.751362 · Cited by 95 · see citing works

BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations

Fu, H., Chen, H., Cai, W., Shao, X., & Chipot, C. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00269 · Cited by 83 · see citing works

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 · see citing works

Skywalker-TBC1D24 has a lipid-binding pocket mutated in epilepsy and required for synaptic function

Fischer, B., Lüthy, K., Paesmans, J., De Koninck, C., Maes, I., Swerts, J., Kuenen, S., Uytterhoeven, V., Verstreken, P., & Versées, W. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3297 · Cited by 62 · see citing works

Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT

Jiang, Y., Benz, T. L., & Long, S. B. (2021) · Science · doi:10.1126/science.abg4998 · Cited by 55 · see citing works

The Q61H mutation decouples KRAS from upstream regulation and renders cancer cells resistant to SHP2 inhibitors

Gebregiworgis, T., Kano, Y., St-Germain, J., Radulovich, N., Udaskin, M. L., Mentes, A., Huang, R., Poon, B. P. K., He, W., Valencia-Sama, I., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26526-y · Cited by 49 · see citing works

Behavior of Citrate-Capped Ultrasmall Gold Nanoparticles on a Supported Lipid Bilayer Interface at Atomic Resolution

Kariuki, R., Penman, R., Bryant, S. J., Orrell-Trigg, R., Meftahi, N., Crawford, R. J., McConville, C. F., Bryant, G., Voïtchovsky, K., Conn, C. E., et al. (2022) · ACS Nano · doi:10.1021/acsnano.2c07751 · Cited by 41 · see citing works

Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake

Long, T., Li, D., Vale, G., Jiang, Y., Schmiege, P., Yang, Z. J., McDonald, J. G., & Li, X. (2024) · Cell · doi:10.1016/j.cell.2024.08.004 · Cited by 31 · see citing works

Characterization of drug binding within the HCN1 channel pore

Tanguay, J., Callahan, K. M., & D’Avanzo, N. (2019) · Scientific Reports · doi:10.1038/s41598-018-37116-2 · Cited by 29 · see citing works

Ketamine Metabolite (2<i>R</i>,6<i>R</i>)-Hydroxynorketamine Interacts with μ and κ Opioid Receptors

Joseph, T. T., Bu, W., Lin, W., Zoubak, L., Yeliseev, A., Liu, R., Eckenhoff, R. G., & Brannigan, G. (2021) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.0c00741 · Cited by 28 · see citing works

Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome

Peck Justice, S. A., Barron, M. P., Qi, G. D., Wijeratne, H. R. S., Victorino, J. F., Simpson, E. R., Vilseck, J. Z., Wijeratne, A. B., & Mosley, A. L. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra120.014576 · Cited by 28 · see citing works

Temperature sensitive Mutant Proteome Profiling: a novel tool for the characterization of the global impact of missense mutations on the proteome

Peck Justice, S. A., Qi, G., Wijeratne, H. R. S., Victorino, J. F., Simpson, E. R., Wijeratne, A. B., & Mosley, A. L. (2019) · doi:10.1101/2019.12.30.891267 · Cited by 28 · see citing works

Design, synthesis, and in vitro and in vivo characterization of new memantine analogs for Alzheimer’s disease

Turcu, A. L., Companys-Alemany, J., Phillips, M. B., Patel, D. S., Griñán-Ferré, C., Loza, M. I., Brea, J. M., Pérez, B., Soto, D., Sureda, F. X., et al. (2022) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2022.114354 · Cited by 27 · see citing works

Hazardous Shortcuts in Standard Binding Free Energy Calculations

Blazhynska, M., Goulard Coderc de Lacam, E., Chen, H., Roux, B., & Chipot, C. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c01490 · Cited by 27 · see citing works

Antibody affinity maturation by computational design

Kuroda, D., & Tsumoto, K. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8648-4_2 · Cited by 26 · see citing works

2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop.

Tanaka, Y., Izumioka, A., Abdul Hamid, A., Fujii, A., Haruyama, T., Furukawa, A., & Tsukazaki, T. (2018) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2018.09.043 · Cited by 23 · see citing works

Characterization of the membrane interactions of phospholipase Cγ reveals key features of the active enzyme

Le Huray, K. I. P., Bunney, T. D., Pinotsis, N., Kalli, A. C., & Katan, M. (2022) · Science Advances · doi:10.1126/sciadv.abp9688 · Cited by 21 · see citing works

Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots

Nordquist, E. B., Zhao, M., Kumar, A., & MacKerell, A. D. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01189 · Cited by 15 · see citing works

A Putative Binding Model of Nitazene Derivatives at the μ-Opioid Receptor

Clayton, J., Shi, L., Robertson, M. J., Skiniotis, G., Michaelides, M., Stavitskaya, L., & Shen, J. (2025) · Neuropharmacology · doi:10.1016/j.neuropharm.2025.110437 · Cited by 12 · see citing works

Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor

Berksoz, M., & Atilgan, C. (2024) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26688 · Cited by 8 · see citing works

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 · see citing works

Human metabolism and pharmacological profiling of protonitazepyne and metonitazepyne, two highly potent nitazenes: prediction of main metabolite activity based on µ-opioid receptor docking simulations

Berardinelli, D., Taoussi, O., Ovat, D. Y., Pichini, S., Pulver, B., Auwärter, V., Busardò, F. P., Basile, G., Laudadio, E., & Carlier, J. (2026) · Archives of Toxicology · doi:10.1007/s00204-025-04163-4 · Cited by 5 · see citing works

The impact of glycosylation on the conformational ensembles of β-, δ-, and γ-sarcoglycans

Fazelpour, E., Cook, G. A., & McCullagh, M. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.04.018

Mobile barrier mechanisms for Na+-coupled symport in an MFS sugar transporter

Hariharan, P., Shi, Y., Katsube, S., Willibal, K., Burrows, N. D., Mitchell, P., Bakhtiiari, A., Stanfield, S., Pardon, E., Kaback, H. R., et al. (2024) · doi:10.7554/elife.92462.2

Fusion of lipid membranes: an alternative pathway

Jin, D., Li, Z., Roke, S., & Klein, J. (2026) · doi:10.64898/2026.02.19.706911