Publications
| 45. | Jakob P. Ulmschneider* & Martin B. Ulmschneider, Melittin can permeabilize membranes via large transient pores, Nature Communications 2024, (15), 7281 |
| 44. | Ayesha Khan, Richard Killick, Daniel Wirth, Dominique Hoogland, Kalina Hristova, J. P. Ulmschneider, Christopher R. King, & Martin B. Ulmschneider. Masking the transmembrane region of the β-amyloid precursor protein as a safe means to lower β-amyloid production Alzheimer's & Dementia: Translational Research & Clinical Interventions. 2023, 9, e12428. |
| 43. | Christian Jorgensen, Evan P. Troendle, J. P. Ulmschneider, Peter C. Searson, Martin B. Ulmschneider: A least-squares-fitting procedure for an efficient preclinical ranking of passive transport across the blood–brain barrier endothelium. Journal of Computer-Aided Molecular Design 2023, 10.1007 |
| 42. | Chen CH, Zan B, J. P. Ulmschneider, Wimley WC, Lu TK, Ulmschneider MB, Zhou L: Development of membrane-active peptide therapeutics in oncology. Journal of Peptide Science 2023, e3482. |
| 41. | Erik Strandberg, Parvesh Wadhwani, Jochen Bürck, Patrick Anders, Christian Mink, Jonas van den Berg, Raffaele A. M. Ciriello, Manuel N. Melo, Miguel A. R. B. Castanho, Eduard Bardaji, J. P. Ulmschneider, and Anne S. Ulrich. Temperature-Dependent Re-alignment of the Short Multifunctional Peptide BP100 in Membranes Revealed by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations. ChemBioChem 2022, e202200602 |
| 40. | Chen CH, Yu-Han Liu, Arvin Eskandari, Jenisha Ghimire, Leon Chien-Wei Lin, Zih-Syun Fang, William C. Wimley, Ulmschneider JP, Kogularamanan Suntharalingam, Che-Ming Jack Hu, and Martin B. Ulmschneider. Integrated Design of a Membrane-Lytic Peptide-Based Intravenous Nanotherapeutic Suppresses Triple-Negative Breast Cancer, Advanced Science 2022, 2105506 |
| 39. | Chen CH*, Charles G. Starr, Shantanu Guha, William C. Wimley, Martin B. Ulmschneider*, Ulmschneider JP*, Tuning of a membrane-perforating antimicrobial peptide to selectively target membranes of different lipid composition The Journal of Membrane Biology 2021, 254, 75-96 |
| 38. | Chen CH, Ulmschneider JP*, Ulmschneider MB: Mechanisms of a Small Membrane-Active Antimicrobial Peptide from Hyla punctata. Australian Journal of Chemistry 2020, 73:236-245. |
| 37. | Chen CH, Melo MCR, Berglund N, Khan A, de la Fuente-Nunez C, Ulmschneider JP*, Ulmschneider MB: Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly. Current Opinion in Structural Biology 2020, 61:160-166 |
| 36. | C.H. Chen, C.G. Starr, E. Troendle, G. Wiedman, W.C. Wimley, J.P. Ulmschneider*, M.B. Ulmschneider. Simulation-guided rational de novo design of a small pore-forming antimicrobial peptide, J. Am. Chem. Soc. 2019, 141, 12, 4839-4848 |
| 35. | Song Ke, M. B. Ulmschneider, A. Wallace, Ulmschneider, J. P*., Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel Biophysical Journal 2018, 115, 1920-193 |
| 34. | Ulmschneider, J. P.*, J. C. Smith, S. H. White, and M. B. Ulmschneider. The importance of the membrane interface as the reference state for membrane protein stability. Biochim. Biophys. Acta Biomem. 2018, 1860(12):2539-2548. |
| 33. | Ulmschneider, J. P.*, & Ulmschneider, M. B. Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes. Accounts of Chemical Research 2018. doi: 10.1021/acs.accounts.7b00613 |
| 32. | Gumbart, J. C., Ulmschneider, M. B., Hazel, A., White, S. H., & Ulmschneider, J. P.* Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. The Journal of Membrane Biology 2018. doi: 10.1007/s00232-018-0026-y |
| 31. | Ulmschneider, J. P.* Highly charged antimicrobial peptides can permeabilize and translocate across lipid bilayers without forming channel-like pores. Biophysical Journal 2017, 113(1), 73-81 |
| 30. | Ulmschneider, M. B., Ulmschneider, J. P., Freites, J. A., von Heijne, G., Tobias, D. J., & White, S. H. Transmembrane helices containing a charged arginine are thermodynamically stable. European Biophysics Journal, 2017, 1-11 |
| 29. | Wang, Y., Chen, C. H., Hu, D., Ulmschneider, M. B. & Ulmschneider, J. P.* Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide. Nature Communications 2016, 7, 13535 |
| 28. | S. Upadhyay, Y. Wang, T. Zhao, J.P. Ulmschneider*, Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers. J Membrane Biol 2015, 248, 497-503 |
27. |
M. B.Ulmschneider, J. P. Ulmschneider, N. Schiller, B.A. Wallace, G. von Heijne & S. H. White Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion Nature Communications 2014, 5:4863 |
26. |
Y. Wang, T. Zhao, D. Wei, E. Strandberg, A. S. Ulrich, J. P. Ulmschneider* How reliable are molecular dynamics simulations of membrane active antimicrobial peptides? BBA Biomembranes, 2014, 1838, 2280 |
25. |
J. P. Ulmschneider* New Insights into the Peptide-Membrane Partitioning Equilibrium from in Silico Free Surface-to-Bilayer Peptide Insertion. Chap. 5 In Liposomes, Lipid Bilayers and Model Membranes: From Basic Research to Application, edited by N. Kučerka G. Pabst, M.-P. Nieh, J. Katsaras CRC Press, 2014 |
24. |
R. McNulty, J. P. Ulmschneider, H. Luecke, M. B. Ulmschneider Mechanisms of molecular transport through the urea channel of Helicobacter pylori Nature Communications 2013, 4:2900 |
23. |
M. Andersson, J. P. Ulmschneider, M. B. Ulmschneider, S. H. White Conformational states of melittin at a bilayer interface, Biophysical Journal 2013, 104, L12 |
22. |
M.B. Ulmschneider, C. Bagnéris, E.C. McCusker, P. DeCaen, M. Delling, D.E. Clapham, J.P. Ulmschneider*, B. A. Wallace, Molecular Dynamics of Ion Transport through the Open Conformation of a Bacterial Voltage-gated Sodium Channel, Proc. Nat. Acad. Sci. 2013, 110, 6364 |
21. |
Y. Wang, D-Q. Wei, R. Gu, H. Fan, J. P. Ulmschneider*, Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems, Canadian Journal of Chemistry 2013, 91(9): 769-774 |
20. |
J. P. Ulmschneider*, Jeremy C. Smith, Martin B. Ulmschneider, Anne S. Ulrich, Erik Strandberg, Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations, Biophysical Journal 2012, (103), Issue 3, 472-482 |
19. |
J.P. Ulmschneider*, J.C. Smith, S. H. White, M. B. Ulmschneider, In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides Under Equilibrium Conditions, J. Am. Chem. Soc. 2011, 133(39):15487-15495. |
18. |
J.P. Ulmschneider*, M. Anderson, M.B. Ulmschneider, Peptide partitioning properties from direct insertion via molecular mechanics simulation, J. Membr. Biol. 2011, 239, 15–26. |
17. |
M.B. Ulmschneider, J.C. Smith, J.P. Ulmschneider*, Peptide partitioning properties from direct insertion studies, Biophys J., 2010, 98, L60–L62. |
16. |
M.B. Ulmschneider, J. P. F. Doux, J. A. Killian, J.C. Smith, J.P. Ulmschneider*, Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides, J. Am. Chem. Soc., 2010, 132, 3452–3460. |
15. |
M.B. Ulmschneider, J.P. Ulmschneider*, Implicit membrane models for peptide folding and insertion studies. In: Molecular Simulations and Biomembranes: From Biophysics to Function, Royal Society of Chemistry, 2010. |
14. |
J. P. Ulmschneider*, J. P. F. Doux, J. A. Killian, J. C. Smith, M. B. Ulmschneider, Peptide Partitioning and Folding into Lipid Bilayers, J. Chem. Theory Comput. 2009, 5, 2202-2205. |
13. |
J.P. Ulmschneider*, M.B. Ulmschneider, United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field. J. Chem. Theory Comput. 2009, 5, 1803-1813. |
12. |
J.P. Ulmschneider*, M.B. Ulmschneider, Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations. Proteins 2009, 75, 586-597. |
11. |
M.B. Ulmschneider, J.P. Ulmschneider*, Folding peptides into lipid bilayers. J. Chem. Theory Comput. 2008, 4, 1807-1809. |
10. |
M.B. Ulmschneider, J.P. Ulmschneider*, Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides, Mol. Mem. Biol. 2008, 25, 245-257. |
9. |
J.P. Ulmschneider*, M.B. Ulmschneider, Folding simulations of the trans-membrane helix of virus protein U in an implicit membrane model. J. Chem. Theory Comput. 2007, 3, 2335-2346. |
8. |
J.P. Ulmschneider*, M.B.Ulmschneider, A. Di Nola, Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane, Proteins 2007, 69, 297-308. |
7. |
M.B.Ulmschneider, J.P. Ulmschneider*, A. Di Nola, M.S.P. Sansom, A generalized Born implicit membrane representation based on experimental insertion free energies. Biophys. J. 2007, 92, 2338–2349. |
6. |
J.P. Ulmschneider*, M.B. Ulmschneider, A. Di Nola, Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding Simulations, J. Phys. Chem. B 2006, 110, 16733-16742. |
5. |
J.P. Ulmschneider, W.L. Jorgensen, Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation, Yale Univ. Ph.D. Thesis, Dec. 2004. |
4. |
W.L. Jorgensen, J.P. Ulmschneider, J. Tirado-Rives, Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field, J. Phys. Chem. B 2004, 108, 16264-16270. |
3. |
J.P. Ulmschneider, W.L. Jorgensen, Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation, J. Am. Chem. Soc. 2004, 126, 1849-1857. |
2. |
J.P. Ulmschneider, W.L. Jorgensen, Monte Carlo Backbone Sampling for Nucleic Acids using Concerted Rotations including Variable Bond Angles, J. Phys. Chem. B 2004, 108, 16883-16892. |
1. |
J.P. Ulmschneider, W.L. Jorgensen, Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias, J. Chem. Phys. 2003, 118, 4261-4271. |
(*corresponding author)