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

Polymorphic transitions in single crystals: A new molecular dynamics method

Parrinello, M., & Rahman, A. (1981) · Journal of Applied Physics · doi:10.1063/1.328693 · Cited by 19,668 · see citing works

LINCS: A linear constraint solver for molecular simulations

Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199709)18:12 · Cited by 18,369 · see citing works

Canonical sampling through velocity rescaling

Bussi, G., Donadio, D., & Parrinello, M. (2007) · The Journal of Chemical Physics · doi:10.1063/1.2408420 · Cited by 18,034 · see citing works

SWISS-MODEL: homology modelling of protein structures and complexes

Waterhouse, A. M., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T., Rempfer, C., Bordoli, L., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky427 · Cited by 13,005 · see citing works

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

Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.20945 · Cited by 9,284 · see citing works

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

Miyamoto, S., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130805 · Cited by 7,268 · see citing works

CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins

Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 6,708 · see citing works

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1100 · Cited by 6,372 · see citing works

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J., Dror, R., & Shaw, D. (2010) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22711 · Cited by 6,037 · see citing works

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations

Marrink, ‪. J., Risselada, H. J., Yefimov, S., Tieleman, D. P., & de Vries, A. H. (2007) · The Journal of Physical Chemistry B · doi:10.1021/jp071097f · Cited by 5,527 · see citing works

Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides

Kaminski, G. A., Friesner, R. A., Tirado‐Rives, J., & Jorgensen, W. L. (2001) · The Journal of Physical Chemistry B · doi:10.1021/jp003919d · Cited by 4,077 · see citing works

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6

Oostenbrink, C., Villa, A., Mark, A. E., & A, W. F. V. G. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20090 · Cited by 3,726 · see citing works

The MARTINI Coarse-Grained Force Field: Extension to Proteins

Monticelli, L., Kandasamy, S. K., Périole, X., Larson, R. G., Tieleman, D. P., & Marrink, ‪. J. (2008) · Journal of Chemical Theory and Computation · doi:10.1021/ct700324x · Cited by 2,491 · see citing works

SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells

Sachs, P., Ding, D., Bergmaier, P., Lamp, B., Schlagheck, C., Finkernagel, F., Nist, A., Stiewe, T., & Mermoud, J. E. (2019) · Nature Communications · doi:10.1038/s41467-019-09078-0 · Cited by 2,388 · see citing works

PHD1 controls muscle mTORC1 in a hydroxylation-independent manner by stabilizing leucyl tRNA synthetase

D’Hulst, G., Soro-Arnaiz, I., Masschelein, E., Veys, K., Fitzgerald, G., Smeuninx, B., Kim, S., Deldicque, L., Blaauw, B., Carmeliet, P., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13889-6 · Cited by 2,310 · see citing works

Genome‐wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

Wallin, E. J., & von HEIJNE, G. (1998) · Protein Science · doi:10.1002/pro.5560070420 · Cited by 1,536 · see citing works

‘Improved parameters for the Martini coarse-grained protein force field’

de Jong, D. H., Singh, G., Bennett, W. F. D., Arnarez, C., Wassenaar, T. A., Schäfer, L. V., Periole, X., Tieleman, D. P., & Marrink, S. J. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct300646g · Cited by 1,486 · see citing works

Arabidopsis PROTEASOME REGULATOR1 is required for auxin-mediated suppression of proteasome activity and regulates auxin signalling

Yang, B.-J., Han, X., Yin, L.-L., Xing, M., Xu, Z. H., & Xue, H. (2016) · Nature Communications · doi:10.1038/ncomms11388 · Cited by 1,203 · see citing works

A Multiscale Coarse-Graining Method for Biomolecular Systems

Izvekov, S., & Voth, G. A. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp044629q · Cited by 1,192 · see citing works

Coarse-Grained Protein Models and Their Applications

Kmiecik, S., Gront, D., Koliński, M., Wieteska, Ł., Badaczewska-Dawid, A. E., & Koliński, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00163 · Cited by 1,067 · see citing works

Heterogeneous Parallelization and Acceleration of Molecular Dynamics Simulations in GROMACS

Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B., & Lindahl, E. (2020) · Journal of Chemical Physics · doi:10.1063/5.0018516 · Cited by 886 · see citing works

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

Wassenaar, T. A., Pluháčková, K., Böckmann, R. A., Marrink, ‪. J., & Tieleman, D. P. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400617g · Cited by 711 · see citing works

Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2

Hansen, S. B., Tao, X., & MacKinnon, R. (2011) · Nature · doi:10.1038/nature10370 · Cited by 628 · see citing works

Molecular control of δ-opioid receptor signalling

Fenalti, G., Giguère, P. M., Katritch, V., Huang, X., Thompson, A. A., Cherezov, V., Roth, B. L., & Stevens, R. C. (2014) · Nature · doi:10.1038/nature12944 · Cited by 501 · see citing works

Setting up and running molecular dynamics simulations of membrane proteins

Kandt, C., Ash, W. L., & Tieleman, D. P. (2007) · Methods · doi:10.1016/j.ymeth.2006.08.006 · Cited by 473 · see citing works

g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation

Wolf, M. G., Hoefling, M., Aponte-Santamaria, C. A., Grubmüller, H., & Groenhof, G. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21507 · Cited by 373 · see citing works

Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins

Corradi, V., Mendez-Villuendas, E., Ingólfsson, H. I., Gu, R., Siuda, I., Melo, M. N., Moussatova, A., DeGagné, L. J., Sejdiu, B. I., Singh, G., et al. (2018) · ACS Central Science · doi:10.1021/acscentsci.8b00143 · Cited by 360 · see citing works

Structural basis for lipopolysaccharide insertion in the bacterial outer membrane

Qiao, S., Luo, Q., Zhao, Y., Zhang, X. C., & Huang, Y. (2014) · Nature · doi:10.1038/nature13484 · Cited by 273 · see citing works

The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions

Newport, T. D., Sansom, M. S. P., & Stansfeld, P. J. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1047 · Cited by 236 · see citing works

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

Stansfeld, P. J., & Sansom, M. S. P. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct100569y · Cited by 232 · see citing works

Protein–ligand binding with the coarse-grained Martini model

Souza, P. C. T., Thallmair, S., Conflitti, P., Ramírez-Palacios, C., Alessandri, R., Raniolo, S., Limongelli, V., & Marrink, S. (2020) · Nature Communications · doi:10.1038/s41467-020-17437-5 · Cited by 201 · see citing works

Validation of protein models derived from experiment

Laskowski, R. A., MacArthur, M. W., & Thornton, J. M. (1998) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(98)80156-5 · Cited by 191 · see citing works

Reconstruction of atomistic details from coarse‐grained structures

Rzepiela, A. J., Schäfer, L. V., Goga, N., Risselada, H. J., de Vries, A. H., & Marrink, ‪. J. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21415 · Cited by 189 · see citing works

Novel Structure of the Conserved Gram-Negative Lipopolysaccharide Transport Protein A and Mutagenesis Analysis

Suits, M. D. L., Sperandeo, P., Dehò, G., Polissi, A., & Jia, Z. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.04.045 · Cited by 164 · see citing works

Crystal structures of bacterial lipoprotein localization factors, LolA and LolB

Takeda, K., Miyatake, H., Yokota, N., Matsuyama, S., Tokuda, H., & Miki, K. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg324 · Cited by 148 · see citing works

Structural Basis for SRY-dependent 46-X,Y Sex Reversal: Modulation of DNA Bending by a Naturally Occurring Point Mutation

Murphy, E. C., Zhurkin, V. B., Louis, J. M., Cornilescu, G., & Clore, G. M. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4977 · Cited by 146 · see citing works

Structural basis of unidirectional export of lipopolysaccharide to the cell surface

Owens, T. W., Taylor, R. J., Pahil, K. S., Bertani, B. R., Ruiz, N., Kruse, A. C., & Kahne, D. E. (2019) · Nature · doi:10.1038/s41586-019-1039-0 · Cited by 140 · see citing works

Structure and Functional Analysis of LptC, a Conserved Membrane Protein Involved in the Lipopolysaccharide Export Pathway in Escherichia coli*

Tran, A. X., Dong, C., & Whitfield, C. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.144709 · Cited by 133 · see citing works

Backmapping triangulated surfaces to coarse-grained membrane models

Pezeshkian, W., König, M., Wassenaar, T., & Marrink, S. (2020) · Nature Communications · doi:10.1038/s41467-020-16094-y · Cited by 129 · see citing works

Computational modeling of membrane proteins

Leman, J. K., Ulmschneider, M. B., & Gray, J. J. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24703 · Cited by 99 · see citing works

Insights into Membrane Protein–Lipid Interactions from Free Energy Calculations

Corey, R. A., Vickery, O. N., Sansom, M. S. P., & Stansfeld, P. J. (2019) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b00548 · Cited by 94 · see citing works

Crystal structure of E. coli lipoprotein diacylglyceryl transferase

Mao, G., Zhao, Y., Kang, X., Li, Z., Zhang, Y., Wang, X., Sun, F., Sankaran, K., & Zhang, X. C. (2016) · Nature Communications · doi:10.1038/ncomms10198 · Cited by 92 · see citing works

Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids

Grote, F., & Lyubartsev, A. P. (2020) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c06386 · Cited by 84 · see citing works

Exploring GPCR–Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward

Sengupta, D., Prasanna, X., Mohole, M., & Chattopadhyay, A. (2018) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.8b01657 · Cited by 77 · see citing works

Stability of Asymmetric Lipid Bilayers Assessed by Molecular Dynamics Simulations

Esteban-Martín, S., Risselada, H. J., Salgado, J., & Marrink, ‪. J. (2009) · Journal of the American Chemical Society · doi:10.1021/ja904450t · Cited by 77 · see citing works

Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis

Wiktor, M., Weichert, D., Howe, N., Huang, C., Oliéric, V., Boland, C., Bailey, J., Vogeley, L., Stansfeld, P. J., Buddelmeijer, N., et al. (2017) · Nature Communications · doi:10.1038/ncomms15952 · Cited by 66 · see citing works

Machine learning approach for accurate backmapping of coarse-grained models to all-atom models

An, Y., & Deshmukh, S. A. (2020) · Chemical Communications · doi:10.1039/d0cc02651d · Cited by 65 · see citing works

A lipid gating mechanism for the channel-forming O antigen ABC transporter

Caffalette, C. A., Corey, R. A., Sansom, M. S. P., Stansfeld, P. J., & Zimmer, J. (2019) · Nature Communications · doi:10.1038/s41467-019-08646-8 · Cited by 56 · see citing works

Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers

Naughton, F. B., Kalli, A. C., & Sansom, M. S. P. (2016) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.6b00153 · Cited by 49 · see citing works

Structures of lipoprotein signal peptidase II from Staphylococcus aureus complexed with antibiotics globomycin and myxovirescin

Olatunji, S., Yu, X., Bailey, J., Huang, C., Zapotoczna, M., Bowen, K., Remškar, M., Müller, R., Scanlan, E. M., Geoghegan, J. A., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-13724-y · Cited by 47 · see citing works

Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries

Jefferys, E. E., Sands, Z. A., Shi, J., Sansom, M. S. P., & Fowler, P. W. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct501111d · Cited by 42 · see citing works

Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability

Stieffenhofer, M., Bereau, T., & Wand, M. (2021) · APL Materials · doi:10.1063/5.0039102 · Cited by 31 · see citing works

Comprehensive Characterization of Lipid-Guided G Protein-Coupled Receptor Dimerization

Gahbauer, S., & Böckmann, R. A. (2020) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.0c00062 · Cited by 28 · see citing works

Characterizing Membrane Association and Periplasmic Transfer of Bacterial Lipoproteins through Molecular Dynamics Simulations

Rao, S., Bates, G. T., Matthews, C. R., Newport, T. D., Vickery, O. N., & Stansfeld, P. J. (2020) · Structure · doi:10.1016/j.str.2020.01.012 · Cited by 27 · see citing works

Bottom-up Coarse-Graining: Principles and Perspectives

Jin, J., Pak, A. J., Durumeric, A. E. P., Loose, T. D., & Voth, G. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00643 · Cited by 296 · see citing works

Two decades of Martini: Better beads, broader scope

Marrink, S. J., Monticelli, L., Melo, M. N., Alessandri, R., Tieleman, D. P., & Souza, P. C. T. (2023) · WIREs Computational Molecular Science · doi:10.1002/wcms.1620 · Cited by 255 · see citing works

PyLipID: A Python Package for Analysis of Protein–Lipid Interactions from Molecular Dynamics Simulations

Song, W., Corey, R. A., Ansell, T. B., Cassidy, C. K., Horrell, M. R., Duncan, A. L., Stansfeld, P. J., & Sansom, M. S. P. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00708 · Cited by 183 · see citing works

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

Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex

Klug, Y. A., Deme, J. C., Corey, R. A., Renne, M. F., Stansfeld, P. J., Lea, S. M., & Carvalho, P. (2021) · Nature Communications · doi:10.1038/s41467-021-26162-6 · Cited by 84 · see citing works

Identification and assessment of cardiolipin interactions with E. coli inner membrane proteins

Corey, R. A., Song, W., Duncan, A. L., Ansell, T. B., Sansom, M. S. P., & Stansfeld, P. J. (2021) · Science Advances · doi:10.1126/sciadv.abh2217 · Cited by 82 · see citing works

Pragmatic Coarse-Graining of Proteins: Models and Applications

Borges-Araújo, L., Patmanidis, I., Singh, A. P., Santos, L. H., Sieradzan, A. K., Vanni, S., Czaplewski, C. R., Pantano, S., Shinoda, W., Monticelli, L., et al. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00733 · Cited by 78 · see citing works

PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection

Xu, D., Jiang, W., Wu, L., Gaudet, R. G., Park, E., Su, M., Cheppali, S. K., Cheemarla, N. R., Kumar, P., Uchil, P. D., et al. (2023) · Nature · doi:10.1038/s41586-023-06322-y · Cited by 76 · see citing works

Structure, mechanism, and inhibition of Hedgehog acyltransferase

Coupland, C. E., Andrei, S. A., Ansell, T. B., Carrique, L., Kumar, P., Sefer, L., Schwab, R. A., Byrne, E. F. X., Pardon, E., Steyaert, J., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.11.018 · Cited by 55 · see citing works

Facilitating CG Simulations with MAD: The MArtini Database Server

Hilpert, C., Beranger, L., Souza, P. C. T., Vainikka, P. A., Nieto, V., Marrink, S. J., Monticelli, L., & Launay, G. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.2c01375 · Cited by 51 · see citing works

Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery

(2022) · doi:10.1126/sciadv.add1436 · Cited by 49 · see citing works

Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?

Larsen, A. H., John, L., Sansom, M. S. P., & Corey, R. A. (2022) · Bioscience Reports · doi:10.1042/bsr20211406 · Cited by 44 · see citing works

Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery

Qian, R., Xue, J., Xu, Y. C., & Huang, J. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01024 · Cited by 41 · see citing works

Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore

Rao, S., Skulsuppaisarn, M., Strong, L. M., Ren, X., Lazarou, M., Hurley, J. H., & Hummer, G. (2024) · Science Advances · doi:10.1126/sciadv.adj8027 · Cited by 40 · see citing works

Integrating Machine Learning in the Coarse-Grained Molecular Simulation of Polymers

Ricci, E., & Vergadou, N. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c06354 · Cited by 41 · see citing works

Towards design of drugs and delivery systems with the Martini coarse-grained model

Kjølbye, L. R., Pereira, G. P., Bartocci, A., Pannuzzo, M., Albani, S., Marchetto, A., Jiménez‐García, B., Martin, J., Rossetti, G., Cecchini, M., et al. (2022) · QRB Discovery · doi:10.1017/qrd.2022.16 · Cited by 39 · see citing works

Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex

Nygaard, R., Graham, C. L., Dufrisne, M. B., Colburn, J. D., Pepe, J. G., Hydorn, M. A., Corradi, S., Brown, C. M., Ashraf, K. U., Vickery, O. N., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40483-8 · Cited by 38 · see citing works

Molecular Dynamics Simulations of Curved Lipid Membranes

Larsen, A. H. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23158098 · Cited by 38 · see citing works

Glimps: A machine learning approach to resolution transformation for multiscale modeling

Louison, K. A., Dryden, I. L., & Laughton, C. A. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00735 · Cited by 35 · see citing works

Peptidoglycan biosynthesis is driven by lipid transfer along enzyme-substrate affinity gradients

Oluwole, A. O., Corey, R. A., Brown, C. M., Hernández‐Rocamora, V. M., Stansfeld, P. J., Vollmer, W., Bolla, J. R., & Robinson, C. V. (2022) · Nature Communications · doi:10.1038/s41467-022-29836-x · Cited by 34 · see citing works

Structural pathway for PI3-kinase regulation by VPS15 in autophagy

Cook, A. S. I., Chen, M., Nguyen, T. N., Cabezudo, A. C., Khuu, G., Rao, S., Garcia, S. N., Yang, M., Iavarone, A. T., Ren, X., et al. (2025) · Science · doi:10.1126/science.adl3787 · Cited by 34 · see citing works

Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery

Paloncýová, M., Valério, M., dos Santos, R. N., Kührová, P., Šrejber, M., Čechová, P., Dobchev, D. A., Balsubramani, A., Banáš, P., Agarwal, V., et al. (2025) · Molecular Pharmaceutics · doi:10.1021/acs.molpharmaceut.4c00744 · Cited by 33 · see citing works

Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus

Madland, E., Forsberg, Z., Wang, Y., Lindorff‐Larsen, K., Niebisch, A., Modregger, J., Eijsink, V. G. H., Aachmann, F. L., & Courtade, G. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101084 · Cited by 31 · see citing works

LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins

Ansell, T. B., Song, W., Coupland, C. E., Carrique, L., Corey, R. A., Duncan, A. L., Cassidy, C. K., Geurts, M. M. G., Rasmussen, T., Ward, A. B., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43392-y · Cited by 31 · see citing works

Binding of Ca2+-independent C2 domains to lipid membranes: A multi-scale molecular dynamics study

Larsen, A. H., & Sansom, M. S. P. (2021) · Structure · doi:10.1016/j.str.2021.05.011 · Cited by 30 · see citing works

‘Asynchronous reciprocal coupling of Martini 2.2 coarse-grained and CHARMM36 all-atom simulations in an automated multiscale framework’

López, C. A., Zhang, X., Aydin, F., Shrestha, R., Van, Q. N., Stanley, C. B., Carpenter, T. S., Nguyen, K., Patel, L. A., Chen, D., et al. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c00168 · Cited by 18 · see citing works

Dual regulation of IP3 receptors by IP3 and PIP2 controls the transition from local to global Ca2+ signals

Ivanova, A., Atakpa‐Adaji, P., Rao, S., Martí-Solano, M., & Taylor, C. W. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.09.009 · Cited by 22 · see citing works

Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca 2+ -sensor ALG-2

Shukla, S., Chen, W., Rao, S., Yang, S., Ou, C., Larsen, K. P., Hummer, G., Hanson, P. I., & Hurley, J. H. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2318046121 · Cited by 21 · see citing works

Cardiolipin, and not monolysocardiolipin, preferentially binds to the interface of complexes III and IV

Corey, R. A., Harrison, N., Stansfeld, P. J., Sansom, M. S. P., & Duncan, A. L. (2022) · Chemical Science · doi:10.1039/d2sc04072g · Cited by 21 · see citing works

On the emergence of machine-learning methods in bottom-up coarse-graining

Sahrmann, P. G., & Voth, G. A. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2024.102972 · Cited by 20 · see citing works

Backmapping with Mapping and Isomeric Information

Kim, S. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c05593 · Cited by 20 · see citing works

Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer

Sahoo, A. R., Souza, P. C. T., Meng, Z., & Buck, M. (2023) · Structure · doi:10.1016/j.str.2023.03.014 · Cited by 19 · see citing works

Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function

Cui, C., Zhao, L., Kermani, A. A., Du, S., Pipatpolkai, T., Jiang, M., Chittori, S., Tan, Y. Z., Shi, J., Delemotte, L., et al. (2025) · Cell Research · doi:10.1038/s41422-025-01152-1 · Cited by 18 · see citing works

The solute carrier SPNS2 recruits PI(4,5)P2 to synergistically regulate transport of sphingosine-1-phosphate

Tang, H., Li, H. Z., Prakaash, D., Pedebos, C., Qiu, X., Sauer, D. B., Khalid, S., Duerr, K. L., & Robinson, C. V. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.033 · Cited by 18 · see citing works

Switching Go-Martini for Investigating Protein Conformational Transitions and Associated Protein–Lipid Interactions

Yang, S., & Song, C. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c01222 · Cited by 18 · see citing works

A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1

Bartocci, A., Grazzi, A., Awad, N., Corringer, P., Souza, P. C. T., & Cecchini, M. (2024) · Nature Communications · doi:10.1038/s41467-024-53098-4 · Cited by 17 · see citing works

Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications

Koukos, P. I., Dehghani‐Ghahnaviyeh, S., Velez‐Vega, C., Manchester, J. I., Tieleman, D. P., Duca, J. S., Souza, P. C. T., & Cournia, Z. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.3c00604 · Cited by 16 · see citing works

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

Larsen, A. H., Tata, L., John, L., & Sansom, M. S. P. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008807 · Cited by 15 · see citing works

TS2CG as a Membrane Builder

Schuhmann, F., Stevens, J. A., Rahmani, N., Lindahl, I., Brown, C. M., Brasnett, C., Anastasiou, D., Vidal, A. B., Geiger, B. J., Marrink, ‪. J., et al. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00833 · Cited by 14 · see citing works

A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations

Alessandri, R., Thallmair, S., Herrero, C. G., Mera‐Adasme, R., Marrink, ‪. J., & Souza, P. C. T. (2023) · A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules · doi:10.1063/9780735425279_001 · Cited by 14 · see citing works

Improved Protein Dynamics and Hydration in the Martini3 Coarse-Grain Model

Kharche, S., Yadav, M., Hande, V. R., Prakash, S., & Sengupta, D. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00802 · Cited by 14 · see citing works

The Role of Cholesterol in M2 Clustering and Viral Budding Explained

Kolokouris, D., Kalenderoglou, I. E., Duncan, A. L., Corey, R. A., Sansom, M. S. P., & Kolocouris, A. (2024) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.4c01026 · Cited by 14 · see citing works

Building complex membranes with Martini 3

Öztürk, T. N., König, M., Carpenter, T. S., Pedersen, K. B., Wassenaar, T. A., Ingólfsson, H. I., & Marrink, ‪. J. (2024) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2024.03.010 · Cited by 13 · see citing works

Structure of the MlaC-MlaD complex reveals molecular basis of periplasmic phospholipid transport

Wotherspoon, P. J., Johnston, H., Hardy, D. J., Holyfield, R., Bui, S., Ratkevičiūtė, G., Sridhar, P., Colburn, J. D., Wilson, C. B., Colyer, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50615-3 · Cited by 13 · see citing works

Toward atomistic models of intact severe acute respiratory syndrome coronavirus 2 via Martini coarse‐grained molecular dynamics simulations

Wang, D., Li, J., Wang, L., Cao, Y., Kang, B., Meng, X., Li, S., & Song, C. (2023) · Quantitative Biology · doi:10.1002/qub2.20 · Cited by 12 · see citing works

Palmitoylation of the Glucagon-like Peptide-1 Receptor Modulates Cholesterol Interactions at the Receptor–Lipid Microenvironment

Naglekar, A., Chattopadhyay, A., & Sengupta, D. (2023) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.3c05930 · Cited by 12 · see citing works

State-dependent binding of cholesterol and an anionic lipid to the muscle-type Torpedo nicotinic acetylcholine receptor

Ananchenko, A., Gao, R. Y., Dehez, F., & Baenziger, J. E. (2024) · Communications Biology · doi:10.1038/s42003-024-06106-8 · Cited by 12 · see citing works

An S-acylated N-terminus and a conserved loop regulate the activity of the ABHD17 deacylase

Holme, S., Sapia, J. L., Davey, M., Vanni, S., & Conibear, E. (2025) · The Journal of Cell Biology · doi:10.1083/jcb.202405042 · Cited by 12 · see citing works

Deep convolutional neural networks for generating atomistic configurations of multi-component macromolecules from coarse-grained models

Christofi, E., Chazirakis, A., Chrysostomou, C., Nicolaou, M. A., Li, W., Doxastakis, M., & Harmandaris, V. (2022) · The Journal of Chemical Physics · doi:10.1063/5.0110322 · Cited by 11 · see citing works

Recovery from desensitization in GluA2 AMPA receptors is affected by a single mutation in the N-terminal domain interface

Larsen, A. H., Perozzo, A. M., Biggin, P. C., Bowie, D., & Kastrup, J. S. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.105717 · Cited by 11 · see citing works

Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa

Marmont, L. S., Orta, A. K., Baileeves, B. W. A., Sychantha, D., Fernández-Galliano, A., Li, Y. E., Greene, N. G., Corey, R. A., Stansfeld, P. J., Clemons, W., et al. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01603-2 · Cited by 11 · see citing works

Structural insights into terminal arabinosylation of mycobacterial cell wall arabinan

Liu, Y., Brown, C. M., Erramilli, S. K., Su, Y.-C., Guu, S.-Y., Tseng, P., Wang, Y.-J., Duong, N. H., Tokarz, P., Kloss, B., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58196-5 · Cited by 12 · see citing works

An N-glycan on the C2 domain of JAGGED1 is important for Notch activation

Meng, Y., Şanlıdağ, S., Jensen, S. A., Burnap, S. A., Struwe, W. B., Larsen, A. H., Feng, X., Mittal, S., Sansom, M. S. P., Sahlgren, C., et al. (2022) · Science Signaling · doi:10.1126/scisignal.abo3507 · Cited by 11 · see citing works

PyLipID: A Python package for analysis of protein-lipid interactions from MD simulationsPreprint

Song, W., Corey, R. A., Ansell, T. B., Cassidy, C. K., Horrell, M. R., Duncan, A. L., Stansfeld, P. J., & Sansom, M. S. P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.14.452312 · Cited by 11 · see citing works

Physics-Informed Deep Learning Approach for Reintroducing Atomic Detail in Coarse-Grained Configurations of Multiple Poly(lactic acid) Stereoisomers

Christofi, E., Bačová, P., & Harmandaris, V. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01870 · Cited by 10 · see citing works

Plant protein–lipid interfaces studied by molecular dynamics simulations

Neubergerová, M., & Pleskot, R. (2024) · Journal of Experimental Botany · doi:10.1093/jxb/erae228 · Cited by 10 · see citing works

Polymyxin B1 in the Escherichia coli inner membrane: A complex story of protein and lipopolysaccharide-mediated insertion

Weerakoon, D., Marzinek, J. K., Pedebos, C., Bond, P. J., & Khalid, S. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107754 · Cited by 10 · see citing works

Partitioning of fatty acids between membrane and storage lipids controls ER membrane expansion

(2025) · doi:10.1038/s44318-024-00355-3 · Cited by 10 · see citing works

CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions

Grünewald, F., Seute, L., Alessandri, R., König, M., & Kroon, P. C. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c00064 · Cited by 10 · see citing works

MprF from Pseudomonas aeruginosa is a promiscuous lipid scramblase with broad substrate specificity

Hankins, M. T. K., Parrag, M., Garaeva, A. A., Earp, J. C., Seeger, M. A., Stansfeld, P. J., & Bublitz, M. (2025) · Science Advances · doi:10.1126/sciadv.ads9135 · Cited by 10 · see citing works

Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria

Ashraf, K. U., Batista, M., Ansell, T. B., Punetha, A., Rosario-Garrido, S., Firlar, E., Kaelber, J. T., Stansfeld, P. J., & Petrou, V. I. (2025) · Nature Communications · doi:10.1038/s41467-025-65968-6 · Cited by 9 · see citing works

Transition between conformational states of the TREK-1 K2P channel promoted by interaction with PIP2

Panasawatwong, A., Pipatpolkai, T., & Tucker, S. J. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.05.019 · Cited by 9 · see citing works

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

Launay, R., Teppa, E., Martins, C., Abby, S. S., Pierrel, F., André, I., & Esque, J. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms231810323 · Cited by 9 · see citing works

Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins

Zhekova, H. R., Ramirez-Echemendía, D. P., Sejdiu, B. I., Pushkin, A., Tieleman, D. P., & Kurtz, I. (2024) · Biophysical Journal · doi:10.1016/j.bpj.2024.05.013 · Cited by 9 · see citing works

Trends & Opportunities in Visualization for Physiology: A Multiscale Overview

Garrison, L., Kolesár, I., Viola, I., Hauser, H., & Brückner, S. (2022) · Computer Graphics Forum · doi:10.1111/cgf.14575 · Cited by 9 · see citing works

There and back again: bridging meso- and nano-scales to understand lipid vesicle patterning

Cornet, J., Coulonges, N., Pezeshkian, W., Penissat-mahaut, M., Desgrez-Dautet, H., Marrink, ‪. J., Destainville, N., Chavent, M. G., & Manghi, M. (2024) · Soft Matter · doi:10.1039/d4sm00089g · Cited by 8 · see citing works

Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex

Chen, H., Siroy, A., Morales, V., Gurvič, D., Quentin, Y., Balor, S., Abuta’a, Y. A., Marteau, M., Froment, C., Caumont‐Sarcos, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65370-2 · Cited by 8 · see citing works

The Role of C2 Domains in Two Different Phosphatases: PTEN and SHIP2

John, L., Naughton, F. B., Sansom, M. S. P., & Larsen, A. H. (2023) · Membranes · doi:10.3390/membranes13040408 · Cited by 8 · see citing works

Cholesterol-Dependent Dimerization and Conformational Dynamics of EphA2 Receptors: Insights from Coarse-Grained and All-Atom Simulations

Sahoo, A. R., Bhattarai, N., & Buck, M. (2025) · Structure · doi:10.1016/j.str.2025.03.014 · Cited by 7 · see citing works

Conformational dynamics and membrane insertion mechanism of B4GALNT1 in ganglioside synthesis

Welland, J. W. J., Barrow, H. G., Stansfeld, P. J., & Deane, J. E. (2025) · Nature Communications · doi:10.1038/s41467-025-60593-9 · Cited by 7 · see citing works

TMEM63 proteins act as mechanically activated cholesterol modulated lipid scramblases contributing to membrane mechano-resilience

Lin, Y., Zhou, Z., Han, Y., Cheng, D., Wang, H. J., Ju, L. A., Zhang, Y., Cox, C. D., & Corry, B. (2026) · Nature Communications · doi:10.1038/s41467-026-68919-x · Cited by 7 · see citing works

ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling

Bennett, W. F., Bernardi, A., Öztürk, T. N., Ingólfsson, H. I., Fox, S. J., Sun, D., & Maupin, C. M. (2024) · Molecules · doi:10.3390/molecules29153557 · Cited by 7 · see citing works

Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers

Wu, Z., & Biggin, P. C. (2022) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c01251 · Cited by 7 · see citing works

All-atom virus simulations to tackle airborne disease.

Dommer, A., Wauer, N. A., Marrink, S., & Amaro, R. (2025) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2025.103048 · Cited by 5 · see citing works

Multiple-Basin Go-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins

Yang, S., & Song, C. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c00256 · Cited by 6 · see citing works

A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily

Parr, R. J., Santin, Y. G., Ratkevičiūtė, G., Caulton, S. G., Radford, P. M., Gurvič, D., Jenkins, M., Doyle, M. T., Mead, L., Silale, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61633-0 · Cited by 6 · see citing works

Structural basis of outer membrane biogenesis by the TamAB translocase

Yang, B., Fan, R., Batista, M. B., Chen, Y., Duan, X., Wang, R., Li, D., Stansfeld, P. J., Zhang, Z., & Dong, C. (2026) · Nature Communications · doi:10.1038/s41467-025-67115-7 · Cited by 6 · see citing works

HEroBM: A deep equivariant graph neural network for high-fidelity backmapping from coarse-grained to all-atom structures

Angioletti, D., Raniolo, S., & Limongelli, V. (2025) · The Journal of Chemical Physics · doi:10.1063/5.0280330 · Cited by 6 · see citing works

Mechanistic basis of antimicrobial resistance mediated by the phosphoethanolamine transferase MCR-1

Zinkle, A. P., Batista, M. B., Herrera, C. M., Erramilli, S. K., Kloss, B., Ashraf, K. U., Nosol, K., Zhang, G., Cater, R. J., Marty, M. T., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65515-3 · Cited by 5 · see citing works

Polymyxins slow down lateral diffusion of proteins and lipopolysaccharide in the E. coli outer membrane

Prakaash, D., & Khalid, S. (2025) · Communications Biology · doi:10.1038/s42003-025-09161-x · Cited by 5 · see citing works

Structural snapshots of Pseudomonas aeruginosa LptB2FG and LptB2FGC reveal insights into lipopolysaccharide recognition and transport

Fiorentino, F., Cervoni, M., Wang, Y., Urner, L. H., Sauer, J. B., Tran, T. A., Corey, R. A., Rotili, D., Mai, A., Stansfeld, P. J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-66182-0 · Cited by 6 · see citing works

Human class B1 GPCR modulation by plasma membrane lipids

Chao, K., Wong, L., Oqua, A. I., Kalayan, J., Manchanda, Y., Gebbie-Rayet, J. T., Hedger, G., Tomás, A., & Rouse, S. L. (2026) · Communications Biology · doi:10.1038/s42003-025-09445-2 · Cited by 5 · see citing works

Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE

Liu, Y., Brown, C. M., Borges, N., Nobre, R. N., Erramilli, S. K., Dufrisne, M. B., Kloss, B., Giacometti, S. I., Esteves, A. M., Timóteo, C. G., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57843-1 · Cited by 5 · see citing works

Multiscale molecular dynamics simulations predict arachidonic acid binding sites in human ASIC1a and ASIC3 transmembrane domains

Ananchenko, A., & Musgaard, M. (2022) · The Journal of General Physiology · doi:10.1085/jgp.202213259 · Cited by 5 · see citing works

Constraint Decoupled Latent Diffusion for Protein Backmapping

Han, X., Sun, Y., Chen, K., Ren, Y., Liu, K., & Ye, Q. (2025) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.5c01364 · Cited by 5 · see citing works

Challenges of Absolute Binding Free Energies for Membrane Exposed Binding PocketsPreprint

Cook, C., Alibay, I., Anand, N. M., Chudyk, E. I., Knegtel, R. M. A., & Biggin, P. C. (2024) · ChemRxiv · doi:10.26434/chemrxiv-2024-9hwjs · Cited by 5 · see citing works

Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization

Abramsson, M. L., Corey, R. A., Skerle, J. L., Persson, L. J., Anden, O., Oluwole, A. O., Howard, R. J., Lindahl, E., Robinson, C. V., Strisovsky, K., et al. (2025) · eLife · doi:10.7554/elife.104237.3 · Cited by 4 · see citing works

The Erlin1/2 complex is a dynamic scaffold for membrane microdomain assembly on the endoplasmic reticulum

Yan, L., Xu, Z., Yao, Y., Awang, T., Wang, X., Wang, Y., 马成英, Li, N., Song, C., Chen, X.-W., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.03.001 · Cited by 4 · see citing works

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 · see citing works

Toward Atomistic Models of Intact SARS-CoV-2 via Martini Coarse-Grained Molecular Dynamics SimulationsPreprint

Wang, D., Li, J., Wang, L., Cao, Y., Li, S., & Song, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.31.478415 · Cited by 4 · see citing works

ESMAdam: a plug-and-play all-purpose protein ensemble generatorPreprint

Yu, Z., Liu, Y., Lin, G., Jiang, W., & Chen, M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.01.19.633818 · Cited by 4 · see citing works

CCD2MD: A Suite of Packages for Preparing Co-Folded Outputs for Molecular Dynamics Simulations

Blow, K. E., Parrag, M., & Stansfeld, P. J. (2025) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.5c02066 · Cited by 3 · see citing works

Discovery of a novel antibacterial protein from Lactobacillus acidophilus using integrated genomic mining, molecular dynamics, and functional assays

Zhang, Y., Lin, W., Rao, W., He, B., He, T., & Huang, G. (2025) · Food Bioscience · doi:10.1016/j.fbio.2025.107674 · Cited by 3 · see citing works

PI3Kδ is selectively inhibited by roginolisib by stabilizing the C-terminal helix kα12

Vadas, O., Tiede, S., Chaouki, M., Tesmer, L. A., Rao, S., Visentin, R., Grädler, U., Augustin, M., Kiefersauer, R., Gößer, C., et al. (2026) · Nature Communications · doi:10.21203/rs.3.rs-8048396/v1 · Cited by 3 · see citing works

Structural determinants for GPCR-mediated inhibition of TASK K2P channels by diacylglycerol and its dysfunction in disease

Jouen-Tachoire, T. R. H., Proks, P., Seiferth, D., Crowther, K. M., Biggin, P. C., Baukrowitz, T., Schewe, M., & Tucker, S. J. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00710-6 · Cited by 3 · see citing works

Structural basis of signal peptide recognition by the signal peptidase complex

Liaci, A. M., Vismpas, D., Kjølbye, L. R., Skalidis, I., Pereira, G. P., Koh, F., Gröllers‐Mulderij, M., Kotecha, A., Souza, P. C. T., & Förster, F. G. (2026) · Nature Communications · doi:10.1038/s41467-026-73423-3 · Cited by 3 · see citing works

Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW–Penicillin-Binding Protein 3 Complex of Haemophilus influenzae

Alhamwi, A. B., Atılgan, C., & Şensoy, Ö. (2023) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c00127 · Cited by 3 · see citing works

All-Atom Membrane Builder via Multiscale Simulation

Kim, S. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.4c01059 · Cited by 3 · see citing works

Structure and Mechanism of Hedgehog Acyl TransferasePreprint

Coupland, C. E., Andrei, S. A., Ansell, T. B., Carrique, L., Kumar, P., Sefer, L., Schwab, R. A., Byrne, E. F. X., Pardon, E., Steyaert, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.08.451580 · Cited by 3 · see citing works

Ligand-like lipid interactions with membrane proteins: Simulations and machine learning

Hedger, G., Lyman, E. R., & Rouse, S. L. (2026) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2026.103226 · Cited by 2 · see citing works

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

Stansfeld, P. J., & Sansom, M. S. P. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct100569y · Cited by 232 · see citing works

CG2AT2: Recovering Atomistic Details from Coarse Grain Simulations

Vickery, O. N., & Stansfeld, P. J. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2020.11.698

CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations

Marchetto, A., Chaib, Z. S., Rossi, C. A., Ribeiro, R. P., Pantano, S., Rossetti, G., & Giorgetti, A. (2020) · Molecules · doi:10.3390/molecules25245934 · Cited by 19 · see citing works

Multiscale Molecular Dynamics Simulations of Membrane Proteins

Khalid, S., & Bond, P. J. (2012) · Methods in molecular biology · doi:10.1007/978-1-62703-017-5_25 · Cited by 19 · see citing works

Initiating Coarse-Grained MD Simulations for Membrane-Bound Proteins

Buyan, A., & Corry, B. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1843-1_11 · Cited by 3 · see citing works