Computer Simulation in Condensed Matter Research Group. SIMCON

Biosystems: cell membranes, oncogenic proteins and more

 

  1. Hu, Z.; Sha, Z.; Marti, J.; Guo, S.; Tao, S-c. (2025)

    Impact of KRAS-G12 mutations on the KRAS-GTP bound conformational dynamics: structure, free energy barriers and drugging pockets. JACS Au (in press).
  2. Lu, H.; Martí, J.; Faraudo, J. (2025) Probing the Structural Dynamics of the Unbound MAX Protein: Insights from Well-Tempered Metadynamics. J.Chem. Inf. and Modeling (12 pages). https://doi.org/10.1021/acs.jcim.5c02155
  3. Ge, Y.; Lu, H.; Marti, J. (2025) Influence of local ordering in the permeation of Temozolomide through the brain plasmatic membrane. Biophys. Chem. 324, 107457. https://doi.org/10.1016/j.bpc.2025.107457
  4. Siqi Yu, Zheyao Hu, Xiaoting Xu, Xiaoran Liang, Jiayi Shen, Min Liu, Mingxi Lin, Hong Chen, Jordi Marti, Sheng-ce Tao, Zhaowei Xu (2025) c-di-GMP inhibits rRNA methylation and impairs ribosome assembly in the presence of kanamycin. EMBO Reports (Nature Publ. Group) 26, 1367-1384. https://link.springer.com/article/10.1038/s44319-025-00377-w
  5. Hu, Z.; Marti, J. (2025) Unraveling atomic-scale mechanisms of GDP extraction catalyzed by SOS1 in KRAS-G12 and KRAS-D12 oncogenes. Comput. Biol. and Med. 186, 109599 (10 pages). https://doi.org/10.1016/j.compbiomed.2024.109599
  6. Hu, Z.; Marti, J. (2025) Atomic-level mechanisms of abnormal activation in NRAS oncogenes from two-dimensional free energy landscapes. Nanoscale 17, 4047-4057. https://doi.org/10.1039/d4nr03372h
  7. Hu, Z.; Marti, J. (2024) Isomer-sourced structure iteration methods for in silico development of inhibitors: Inducing GTP-bound NRAS-Q61 oncogenic mutations to an “off-like” state. Comput. Struc. Biotech, J. 23, 2418-2428. https://doi.org/10.1016/j.csbj.2024.05.038
  8. Hu, Z.; Marti, J. (2024) In silico drug derivatives for KRAS-G12D: free-energy surfaces in aqueous solution by well-tempered metadynamics simulations. Mol. Phys. 122, e2316883 (15 pages). https://doi.org/10.1080/00268976.2024.2316883
  9. Lu, H.; Hu, Z.; Faraudo, J.; Martí, J. (2023) In silico design of a lipid-like compound targeting KRAS4B-G12D through non-covalent bonds. Nanoscale 15, 19359-19368. DOI: 10.1039/D3NR04513G
  10. Hu, Z.; Marti, J. (2022) Discovering and Targeting Dynamic Drugging Pockets of Oncogenic Proteins: The Role of Magnesium in Conformational Changes of the G12D Mutated Kirsten Rat Sarcoma-Guanosine Diphosphate Complex, International Journal of Molecular Sciences 23, 13865 (2022) (27 pages). https://doi.org/10.3390/ijms232213865
  11. Lu, H.; Marti, J. (2022) Predicting the conformational variability of oncogenic GTP-bound G12D mutated KRas-4B proteins at zwitterionic model cell membranes. Nanoscale 14, 3148 (11 pages).
  12. Marti, J., Calero,C. (2022) Modeling and Simulation of Lipid Membranes. Membranes 12, 549 (4 pages).
  13. Hu, Z.; Marti, J. (2022), In silico drug design of benzothiadiazine derivatives interacting with phospholipid cell membranes, Membranes 12, 331 (17 pages).
  14. Hu, Z.; Marti, J.; Lu, H. (2021), Structure of benzothiadiazine at zwitterionic phospholipid cell membranes, J.Chem. Phys. 155, 154303 (9 pages)
  15. Marti, J.; Lu, H. (2021), Microscopic Interactions of Melatonin, Serotonin and Tryptophan with Zwitterionic Phospholipid Membranes, International Journal of Molecular Sciences 22, 2842 (25 pages)
  16. Lu, H.; Marti, J. (2020), Influence of cholesterol on the orientation of the farnesylated GTP-bound KRas-4B binding with anionic model membranes, Membranes 10, 364 (19 pages)
  17. Lu, H.; Marti, J. (2020), Long-lasting salt bridges provide the anchoring mechanism of oncogenic Kirsten rat sarcoma proteins at cell membranes. J.Phys.Chem.Lett. 11, 9938-9945
  18. Lu, H.; Marti, J. (2020), Cellular absorption of small molecules: free energy landscapes of melatonin binding at

    phospholipid membranes, Scientific Reports (Nature Publ. Group) 10, 9235 (12 pages)

  19. Lu, H.; Marti, J. (2019), Binding and dynamics of melatonin at the interface of phosphatidylcholine-cholesterol membranes, PLos One, 14 (11), e0224624 (20 pages)
  20. Lu, H.; Marti, J. (2018), Effects of cholesterol on the bonding of the precursor neurotransmitter tryptophan to zwitterionic membranes, J.Chem. Phys. 149, 164906 (10 pages)
  21. Lu, H.; Marti, J. (2018), Binding free energies of small-molecules in phospholipid membranes: Aminoacids, serotonin and melatonin, Chem.Phys.Lett. 712, 190-195
  22. Marti, J., (2018), Free-energy surfaces of ionic adsorption in cholesterol-free and cholesterol-rich phospholipid membranes, Molecular simulation, 44, 1136-1146
  23. Marti, J.; Lu, H. (2017), Molecular dynamics of di-palmitoyl-phosphatidyl-choline biomembranes in ionic solution: adsorption of the precursor neurotransmitter tryptophan, Procedia computer science, vol. 108, no. C, pp. 1242-1250
  24. Yang, J., Marti, J., Calero,C. (2016), Pair interactions among ternary DPPC/POPC/cholesterol mixtures in liquid-ordered and liquid-disordered phases. Soft Matter 12, 4557-4561
  25. Yang, J., Bonomi, M., Calero,C., Marti, J. (2016), Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution. Phys. Chem. Chem. Phys. 18, 9036-9041
  26. Yang, J.,Calero, C., Bonomi, M., Marti, J. (2015), Specific Ion Binding at Phospholipid Membrane Surfaces, J.Chem. Theory Comput. 11, 4495-4499.
  27. Yang, J.; Calero, C.; Marti, J. Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes. Journal of chemical physics 140, pp. 104901-1 - 104901-13 (2014).
  28. Rodriguez, J.; Marti, J.; Guardia, E.; Laria, D. Exploring the Picosecond Time Domain of the Solvation Dynamics of Coumarin 153 within beta-Cyclodextrins. Journal of physical chemistry B 112, pp. 8990 - 8998 (2008).
  29. Marti, J. A molecular dynamics transition path sampling study of model lipid bilayer membranes in aqueous environments. Journal of physics: condensed matter 16, pp. 5669 - 5678 (2004).
  30. Marti, J.; Csajka, F. Transition path sampling study of flip-flop transitions in model lipid bilayer membranes. Physical review E, statistical physics, plasmas, fluids, and related interdisciplinary topics 69, 061918, pp. 1 - 7 (2004).
  31. Marti, J.; Csajka, F. Flip-flop dynamics in a model lipid bilayer membrane. Europhysics letters 61, pp. 409 - 414 (2003).
  32. Marti, J. Transition path sampling study of the local molecular structure in the aqueous solvation of sodium-chloride. Molecular simulation 27, pp. 169 - 185 (2001).
  33. Marti, J.; Csajka, F.; Chandler, D. Stochastic transition pathways in th aqueous sodium chloride dissociation process. Chemical physics letters 328, pp. 169 - 176 (2000).
  34. Marti, J.; Csajka, F. The aqueous solvation of sodium chloride: A Monte Carlo transition path sampling study. Journal of chemical physics 113, pp. 1154 - 1161 (2000).
  35. F.S.Csajka; Marti, J.; Chandler, D. Finding reaction pathways of complex systems. Abstracts of papers of the American Chemical Society 213, 99 (1997).