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

Cited by (150)

Items 101–150 of 150

1. Computational Microscopy of Lipid Confined Systems: Challenges and Opportunities
   Petra Čechová, Petra Kührová, Martin Šrejber, Mariana Valério, Mariia Borbuliak, Paulo C. T. Souza, Michal Otyepka, Markéta Paloncýová · 2026 · Small Structures
2. The molecular basis of mitochondrial crista formation by the MIC10 complex
   Chelsea M. Brown, Tsjerk A. Wassenaar, Zachary Freyberg, ‪Siewert J. Marrink · 2026 · Science Advances
3. Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl – Channel
   Linda X. Phan, Aaron P. Owji, Tingting Yang, Jason N. Crain, Mark S.P. Sansom, Stephen J. Tucker · 2025 · Journal of Chemical Theory and Computation
4. ART-SM: Boosting Fragment-Based Backmapping by Machine Learning
   Christian Pfaendner, Viktoria Korn, Pritom Gogoi, Benjamin Unger, Kristýna Pluháčková · 2025 · Journal of Chemical Theory and Computation
5. Computational Elucidation of Sterol Recognition by SREBP Cleavage Activatory Protein
   Charal Khiewdee, Puey Ounjai, Tanadet Pipatpolkai · 2025 · Journal of Chemical Information and Modeling
6. ViSCa: A computational toolbox for vibrational spectral calculations—Application to sum frequency generation spectroscopy of proteins
   Khezar Hayat Saeed, Kris Strunge, Rolf Mertig, Steven Joop Roeters, Tobias Weidner · 2025 · The Journal of Chemical Physics
7. Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
   Mia L. Abramsson, Robin Adam Corey, Jan L Skerle, Louise J Persson, Olivia Andén, Abraham Olusegun Oluwole, Rebecca J. Howard, Erik R. Lindahl, Carol V. Robinson, Kvido Střı́šovský et al. · 2025 · eLife
8. NLRP3 is a thermosensor that is negatively regulated by high temperature
   Wei Wang, Damien Bertheloot, Junya Zhang, Marcia A. Munoz, Shangze Xu, Amelia Stennett, Chloe M. McKee, Ryan Knight, Emma C. McKay, Bernardo S. Franklin et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
9. Force Field-Driven Backmapping for Multiscale Molecular Dynamics
   Xu Guo, Andrew Abi Mansour, P. Ortoleva · 2025 · Journal of Chemical Theory and Computation
10. Surfactant self-assembly and micelle elongation in reline: structural basis and driving forces
    Petteri A. Vainikka, Karen J. Edler · 2026 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
11. Cell surface liposome binding (CLiB) allows lipid-binding probe engineering via high-throughput screening
    Taki Nishimura, Kotaro Tsuboyama, Yuki Nakagaki, Shiou-Ling Lu, Yuki Ishino, Nozomu Kono, Takeshi Noda, Eiji Yamamoto, Noboru Mizushima · 2026 · Nature Cell Biology
12. Encounter-State Over-Anchoring Governs Productive PETase Binding on PET Surfaces
    Chengze Huo, Jun Wang, Xiakun Chu · 2026 · Journal of Chemical Theory and Computation
13. Lysophospholipid–TRPV1 interactions in chemotherapy-induced neuropathy
    Saskia Wedel, Ainara Claveras Cabezudo, Oliver Rauh, Elena Olkhova, Christian Müller, Lisa Hahnefeld, Robert Gurke, Gerd Geißlinger, Gerhard Hummer, Marco Sisignano · 2026 · Proceedings of the National Academy of Sciences
14. A Full-Scaled Perspective of K-Ras4B Transformations Modulated by Oncogenic G12D and Phosphorylation in Phase-Segregated Membrane
    Yanjiao Wang, Yi Zhang, Hao Chen, Xinkai Zhang, Chenlu Wang, Fude Sun · 2025 · Journal of Chemical Information and Modeling
15. Transmembrane region dimer structures of Type 1 receptors readily sample alternate configurations: MD simulations using the Martini 3 coarse grained model compared to AlphaFold2 Multimer
    Amita Rani Sahoo, Paulo C. T. Souza, Zhiyuan Meng, Matthias Buck · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
16. A feedback control mechanism governs the synthesis of lipid-linked precursors of the bacterial cell wall
    Lindsey S. Marmont, Anna K. Orta, Robin Adam Corey, David Sychantha, Ana Fernández-Galliano, Yancheng E. Li, Becca W A Baileeves, Neil G. Greene, Phillip James Stansfeld, William Clemons et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
17. Recent advances in modeling membrane beta-barrel proteins using molecular dynamics simulations: from their lipid environments to their assemblies
    Anna L. Duncan, Ya Gao, Evert Haanappel, Wonpil Im, Matthieu G. Chavent · 2023 · ChemRxiv
18. An acylated N-terminus and a conserved loop regulate the activity of the ABHD17 de-acylase
    Sydney Holme, Jennifer L. Sapia, Michael Davey, Stefano Vanni, Elizabeth Conibear · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
19. The partitioning of fatty acids between membrane and storage lipids controls ER membrane expansion.
    Lysyganicz, Pawel K, Barbosa, Antonio D, Khondker, Shoily, Stewart, Nicholas A, Carman, George M, Stansfeld, Phillip J, Dymond, Marcus K, Siniossoglou, Symeon · 2024
20. Multiple-Basin Gō-Martini for Investigating Conformational Transitions and Environmental Interactions of Proteins
    Song Yang, Chen Song · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
21. Tyrosine phosphorylation and the inhibitory C-terminal SAM domain regulate the EphA2 intracellular fragment in solution: A combined experimental and molecular modeling study
    Pravesh Shrestha, Amita Rani Sahoo, Maria Iannucci, Belinda B. Willard, Matthias Buck · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
22. Structural mechanism of TRPC3 inhibition by a potent and selective antagonist
    Jodie Collingridge, Bethan A. Cole, John Liddle, Kelly M. Gatfield, Philip Charles Biggin, Esther B E Becker · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
23. Molecular determinants of dynamic protein-protein interactions in the functional cycle of the membrane protein DsbD
    Lukas S. Stelzl, Paraskevi Kritsiligkou, Ahmad Reza Mehdipour, Andrew J. Baldwin, Stuart J. Ferguson, Despoina A. I. Mavridou, Mark S.P. Sansom, Christina Redfield · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
24. Recommendation: Towards design of drugs and delivery systems with the Martini coarse-grained model — R1/PR5
    Lisbeth R. Kjølbye, Gilberto P. Pereira, Alessio Bartocci et al. · 2022 · QRB Discovery
25. Recommendation: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR4
    Lisbeth R. Kjølbye, Gilberto P. Pereira, Alessio Bartocci et al. · 2022 · QRB Discovery
26. Review: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR1
    Lisbeth R. Kjølbye, Gilberto P. Pereira, Alessio Bartocci et al. · 2022 · QRB Discovery
27. Review: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR3
    Lisbeth R. Kjølbye, Gilberto P. Pereira, Alessio Bartocci et al. · 2022 · QRB Discovery
28. Review: Towards design of drugs and delivery systems with the Martini coarse-grained model — R0/PR2
    Lisbeth R. Kjølbye, Gilberto P. Pereira, Alessio Bartocci et al. · 2022 · QRB Discovery
29. Recent Advances in Modeling Membrane β-Barrel Proteins Using Molecular Dynamics Simulations: From Their Lipid Environments to Their Assemblies
    Anna L. Duncan, Ya Gao, Evert Haanappel, Wonpil Im, Matthieu G. Chavent · 2024 · Methods in molecular biology
30. Molecular determinant of sterol recognition by sterol cleavage activatory protein
    Charal Khiewdee, Puey Ounjai, Tanadet Pipatpolkai · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
31. Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
    Mia L. Abramsson, Robin Adam Corey, Jan L Skerle, Louise J Persson, Olivia Andén, Abraham Olusegun Oluwole, Rebecca J. Howard, Erik R. Lindahl, Carol V. Robinson, Kvido Střı́šovský et al. · 2025 · eLife
32. Conformational Dynamics and Membrane Insertion Mechanism of B4GALNT1 in Ganglioside Synthesis
    Jack W.J. Welland, Henry G. Barrow, Phillip James Stansfeld, Janet Elwyn Deane · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
33. Engineering cardiolipin binding to an artificial membrane protein reveals determinants for lipid-mediated stabilization
    Mia L. Abramsson, Robin Adam Corey, Jan L Skerle, Louise J Persson, Olivia Andén, Abraham Olusegun Oluwole, Rebecca J. Howard, Erik R. Lindahl, Carol V. Robinson, Kvido Střı́šovský et al. · 2025 · eLife
34. Discovery of a novel antimicrobial protein from Lactobacillus plantarum by computational screening and experimental evaluation
    Yubo Zhang, Weiying Rao, Weiling Lin, Binqi He, Guidong Huang · 2025 · International Journal of Biological Macromolecules
35. SpoIIIL is a forespore factor required for efficient cell-cell signalling during Bacillus subtilis sporulation
    Danae Morales Angeles, Kaitlyn Coleman, Chimezie Progress Odika, Chris LB Graham, Helena Chan, Michael C. Gilmore, Najwa Taïb, Elda Bauda, Christine Moriscot, Benoît Gallet et al. · 2025 · PLoS Genetics
36. Structural determinants for GqPCR-mediated inhibition of TASK K2P K + channels and their dysfunction in disease
    Thibault R. H. Jouen-Tachoire, Peter Proks, David Seiferth, Kate M. Crowther, Philip Charles Biggin, Thomas Baukrowitz, Marcus Schewe, Stephen J. Tucker · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
37. Pathway and gates for ATG2A-mediated lipid transport in autophagy
    Ainara Claveras Cabezudo, Elisabeth Holzer, Sascha Martens, Gerhard Hummer · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
38. Multiscale simulations
    Alexander V. Neimark, Kolattukudy Poulose Santo · 2025 · Elsevier eBooks
39. Efficient sampling of complex biomolecular assemblies using molecular simulations
    Florence Szczepaniak · 2024 · theses.fr (ABES)
40. Engineering phage endolysins and receptor-binding proteins for foodborne pathogen control and detection: A review and AI-driven framework
    Zongcheng Wu, Xiaofeng Yu, Honglin Ren, Chunyi Shangguan, Cheng Han, Xi Yang, Shuaihao Qi, Xuepeng Duan, Han Wang, Pan Hu et al. · 2026 · International Journal of Food Microbiology
41. CTGoMartini : A Python Framework for Simulating Biomolecular Conformational Transitions with Gō-Martini Models
    Song Yang, Chen Song · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
42. Structure and substrate recognition by the bacterial twin-arginine translocation (Tat) core complex
    Justin C. Deme, Owain J. Bryant, Mariana Batista, Phillip James Stansfeld, Ben C. Berks, Susan M. Lea · 2026 · Nature Microbiology
43. Phosphorylation-dependent Remodeling of the CLOCK–BMAL1–nucleosome Complex
    Dima Amairy, Hanife Pekel, Şeref Gül, Özge Şensoy · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
44. Competitive Interfacial Partitioning in Cetyltrimethylammonium Bromide Self‐Assembly: A Coarse‐Grained Study Across Deep Eutectic Solvents
    Petteri A. Vainikka, Karen J. Edler · 2026 · ChemistryOpen
45. An automated clustering workflow for molecular simulation data
    Elena Paulus, Madlen Malcharek, Christine Peter · 2026 · The Journal of Chemical Physics
46. Structural mechanism of nuclear membrane sealing by LEM2-ESCRT-III
    Mareike A. Jordan, Karen Palacio‐Rodríguez, Ramesh Adakkattil, Sonja Welsch, Lukas Niese, Dollie LaJoie, Esther von der Weth, Arthur Alves de Melo, Lisa Redlingshöfer, Shotaro Otsuka et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
47. Distinct Lipid Binding Dynamics and Sodium Ion Coordination in the TRAP Transporter Hi SiaQM Revealed by Multiscale Molecular Dynamics Simulations
    Senwei Quan, James S. Davies, Rachel A. North, Kelsi R. Hall, Liam S. Turk, Michael C. Newton-Vesty, Renwick C. J. Dobson, Jane R. Allison · 2026 · Journal of Chemical Information and Modeling
48. Sequence variations govern the hierarchical self-assembly and structural polymorphism of PSM-α functional amyloids
    Fengjuan Huang, Yiran Wang, Hao Sun, Huan Xu, Chuang Wang, Yan Chen, Feng Ding, Yunxiang Sun · 2026 · Colloids and Surfaces B Biointerfaces
49. Structural mechanism of TRPC3 inhibition by a potent antagonist
    Jodie Collingridge, Bethan A. Cole, Molly A. Rowlett, John Liddle, Kelly M. Gatfield, Philip Charles Biggin, Esther B. E. Becker · 2026 · Journal of Biological Chemistry
50. VASP association stabilizes the actin nucleus revealed by molecular dynamics simulations
    Xiaoting Li, Jie Hu, Yu Sun, Congfei Xu, 付义本 · 2026 · bioRxiv (Cold Spring Harbor Laboratory)