Publications

Recent Press Coverage

Our successes in the field of membrane active peptides have been recently highlighted:

Tieleman, D. P., New and Notable: Antimicrobial Peptides in the Cross Hairs of Computer Simulations.
Biophysical Journal, 2017, 113(1), 1-3

(*corresponding author)

Publications

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.
 
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