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Jakob P. Ulmschneider, Ph.D. - Publications

Affiliations: 
2004 Yale University, New Haven, CT 
Area:
computational chemistry and molecular design
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53 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Chen CH, Zan B, Ulmschneider JP, Wimley WC, Lu TK, Ulmschneider MB, Zhou L. Development of membrane-active peptide therapeutics in oncology. Journal of Peptide Science : An Official Publication of the European Peptide Society. e3482. PMID 36739581 DOI: 10.1002/psc.3482  0.398
2022 Strandberg E, Wadhwani P, Bürck J, Anders P, Mink C, van den Berg J, Ciriello RAM, Melo MN, Castanho MARB, Bardaji E, Ulmschneider JP, Ulrich AS. Temperature-dependent re-alignment of the short multifunctional peptide BP100 in membranes revealed by solid-state NMR and molecular dynamics simulations. Chembiochem : a European Journal of Chemical Biology. PMID 36454659 DOI: 10.1002/cbic.202200602  0.46
2022 Chen CH, Pepper K, Ulmschneider JP, Ulmschneider MB, Lu TK. Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes. Methods in Molecular Biology (Clifton, N.J.). 2405: 115-136. PMID 35298811 DOI: 10.1007/978-1-0716-1855-4_6  0.506
2022 Chen CH, Liu YH, Eskandari A, Ghimire J, Lin LC, Fang ZS, Wimley WC, Ulmschneider JP, Suntharalingam K, Hu CJ, Ulmschneider MB. Integrated Design of a Membrane-Lytic Peptide-Based Intravenous Nanotherapeutic Suppresses Triple-Negative Breast Cancer. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2105506. PMID 35246961 DOI: 10.1002/advs.202105506  0.332
2021 Chen CH, Starr CG, Guha S, Wimley WC, Ulmschneider MB, Ulmschneider JP. Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition. The Journal of Membrane Biology. PMID 33564914 DOI: 10.1007/s00232-021-00174-1  0.459
2020 Chen CH, Melo MC, Berglund N, Khan A, de la Fuente C, Ulmschneider JP, Ulmschneider MB. Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly. Current Opinion in Structural Biology. 61: 160-166. PMID 32006812 DOI: 10.1016/J.Sbi.2019.12.021  0.567
2020 Chen CH, Ulmschneider JP, Ulmschneider MB. Mechanisms of a Small Membrane-Active Antimicrobial Peptide from Hyla punctata Australian Journal of Chemistry. 73: 236. DOI: 10.1071/Ch19429  0.547
2019 Chen C, Starr CG, Troendle EP, Wiedman G, Wimley WC, Ulmschneider JP, Ulmschneider MB. Simulation-guided rational de novo design of a small pore-forming antimicrobial peptide. Journal of the American Chemical Society. PMID 30839209 DOI: 10.1021/Jacs.8B11939  0.533
2018 Ke S, Ulmschneider MB, Wallace BA, Ulmschneider JP. Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel. Biophysical Journal. PMID 30366630 DOI: 10.1016/J.Bpj.2018.10.001  0.374
2018 Ulmschneider JP, Smith JC, White SH, Ulmschneider MB. The importance of the membrane interface as the reference state for membrane protein stability. Biochimica Et Biophysica Acta. Biomembranes. 1860: 2539-2548. PMID 30293965 DOI: 10.1016/J.Bbamem.2018.09.012  0.519
2018 Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP. Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. The Journal of Membrane Biology. PMID 29943127 DOI: 10.1007/S00232-018-0038-7  0.352
2018 Ulmschneider JP, Ulmschneider MB. Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes. Accounts of Chemical Research. PMID 29667836 DOI: 10.1021/Acs.Accounts.7B00613  0.599
2018 Gumbart JC, Ulmschneider MB, Hazel A, White SH, Ulmschneider JP. Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method. The Journal of Membrane Biology. PMID 29520628 DOI: 10.1007/S00232-018-0026-Y  0.502
2018 Ulmschneider J. Ab-Initio Prediction of Antimicrobial Peptides Channels in Membranes Biophysical Journal. 114: 377a. DOI: 10.1016/J.Bpj.2017.11.2086  0.495
2017 Ulmschneider JP. Charged Antimicrobial Peptides Can Translocate across Membranes without Forming Channel-like Pores. Biophysical Journal. 113: 73-81. PMID 28700927 DOI: 10.1016/J.Bpj.2017.04.056  0.551
2017 Ulmschneider MB, Ulmschneider JP, Freites JA, von Heijne G, Tobias DJ, White SH. Transmembrane helices containing a charged arginine are thermodynamically stable. European Biophysics Journal : Ebj. PMID 28409218 DOI: 10.1007/S00249-017-1206-X  0.555
2017 Chen CH, Starr CG, Wiedman G, Wimley WC, Ulmschneider JP, Ulmschneider MB. Simulation and Database-Guided Antimicrobial Peptide Evolution Biophysical Journal. 112: 382a. DOI: 10.1016/J.Bpj.2016.11.2074  0.466
2017 Ulmschneider JP. How Antimicrobial Peptides Permeabilize Membranes with and without Pore Formation Biophysical Journal. 112: 381a. DOI: 10.1016/J.Bpj.2016.11.2070  0.511
2017 Zhao T, Wang Y, Hu D, Ulmschneider J. Insertion Process of Different Amphipathic α-Helical AMPS into Lipid Bilayers Observed in Unbiased Atomic Molecular Dynamics Simulations Biophysical Journal. 112: 379a. DOI: 10.1016/J.Bpj.2016.11.2061  0.425
2017 Wang Y, Chen C, Hu D, Ulmschneider J, Ulmschneider M. Spontaneous Formation of an Ensemble of Structurally Diverse Membrane Channel Architectures from a Single Antimicrobial Peptide Maculatin Biophysical Journal. 112: 24a. DOI: 10.1016/J.Bpj.2016.11.162  0.51
2016 Wang Y, Chen CH, Hu D, Ulmschneider MB, Ulmschneider JP. Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide. Nature Communications. 7: 13535. PMID 27874004 DOI: 10.1038/Ncomms13535  0.529
2016 Ke S, Wallace BA, Ulmschneider JP, Ulmschneider MB. Molecular Dynamics Simulations of the Open State Structure of a Bacterial Voltage-Gated Sodium Channel Reveal the Binding Mechanisms of Channel Blockers Biophysical Journal. 110: 108a. DOI: 10.1016/J.Bpj.2015.11.640  0.332
2015 Upadhyay SK, Wang Y, Zhao T, Ulmschneider JP. Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers. The Journal of Membrane Biology. 248: 497-503. PMID 25963936 DOI: 10.1016/J.Bpj.2015.11.476  0.573
2015 Wang Y, Gu R, Fan H, Ulmschneider J, Wei D. Applications of rare event dynamics on the free energy calculations for membrane protein systems. Advances in Experimental Medicine and Biology. 827: 71-82. PMID 25387960 DOI: 10.1007/978-94-017-9245-5_6  0.465
2014 Ulmschneider MB, Ulmschneider JP, Schiller N, Wallace BA, von Heijne G, White SH. Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion. Nature Communications. 5: 4863. PMID 25204588 DOI: 10.1038/Ncomms5863  0.565
2014 Wang Y, Zhao T, Wei D, Strandberg E, Ulrich AS, Ulmschneider JP. How reliable are molecular dynamics simulations of membrane active antimicrobial peptides? Biochimica Et Biophysica Acta. 1838: 2280-8. PMID 24747526 DOI: 10.1016/J.Bbamem.2014.04.009  0.538
2014 Ulmschneider JP, Wang Y. Membrane Translocation of Highly Charged Antimicrobial Peptides via Multi-Microsecond All-Atom Md Simulations Biophysical Journal. 106: 297a. DOI: 10.1016/J.Bpj.2013.11.1731  0.519
2013 McNulty R, Ulmschneider JP, Luecke H, Ulmschneider MB. Mechanisms of molecular transport through the urea channel of Helicobacter pylori. Nature Communications. 4: 2900. PMID 24305683 DOI: 10.1038/Ncomms3900  0.351
2013 Ulmschneider MB, Bagnéris C, McCusker EC, Decaen PG, Delling M, Clapham DE, Ulmschneider JP, Wallace BA. Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel. Proceedings of the National Academy of Sciences of the United States of America. 110: 6364-9. PMID 23542377 DOI: 10.1073/Pnas.1214667110  0.359
2013 Andersson M, Ulmschneider JP, Ulmschneider MB, White SH. Conformational states of melittin at a bilayer interface. Biophysical Journal. 104: L12-4. PMID 23528098 DOI: 10.1016/J.Bpj.2013.02.006  0.547
2013 Ulmschneider MB, Bagnéris C, McCusker EC, Ulmschneider JP, Wallace B. Microsecond Molecular Dynamics Simulations of the Open State Structure of a Bacterial Voltage-Gated Sodium Channel Reveal Mechanisms of Ion Selectivity and Conduction Biophysical Journal. 104: 132a-133a. DOI: 10.1016/J.Bpj.2012.11.758  0.379
2012 Ulmschneider JP, Smith JC, Ulmschneider MB, Ulrich AS, Strandberg E. Reorientation and dimerization of the membrane-bound antimicrobial peptide PGLa from microsecond all-atom MD simulations. Biophysical Journal. 103: 472-82. PMID 22947863 DOI: 10.1016/J.Bpj.2012.06.040  0.554
2012 Ulrich AS, Heidenreich N, Wadhwani P, Reichert J, Strandberg E, Misievicz J, Afonin S, Berditsch M, Bürck J, Tiltak D, Ulmschneider J, Benz R, Mangoni M, Castanho M. Short Stories - on Antimicrobial Peptides that are Too Short to Span the Membrane Biophysical Journal. 102: 616a. DOI: 10.1016/J.Bpj.2011.11.3358  0.553
2012 Ulmschneider JP, White SH, Smith J, Ulmschneider MB. The Difference Between Translocon-Assisted Membrane Insertion and Free Surface-To-Bilayer Peptide Insertion Biophysical Journal. 102: 615a. DOI: 10.1016/J.Bpj.2011.11.3355  0.534
2011 Ulmschneider JP, Smith JC, White SH, Ulmschneider MB. In silico partitioning and transmembrane insertion of hydrophobic peptides under equilibrium conditions. Journal of the American Chemical Society. 133: 15487-95. PMID 21861483 DOI: 10.1021/Ja204042F  0.528
2011 Ulmschneider JP, Andersson M, Ulmschneider MB. Determining peptide partitioning properties via computer simulation. The Journal of Membrane Biology. 239: 15-26. PMID 21107546 DOI: 10.1007/S00232-010-9324-8  0.594
2011 Ulmschneider JP. Adsorption and Insertion Kinetics of Membrane Active Peptides from Fully Atomistic Simulations Biophysical Journal. 100: 498a. DOI: 10.1016/J.Bpj.2010.12.2917  0.552
2010 Ulmschneider MB, Smith JC, Ulmschneider JP. Peptide partitioning properties from direct insertion studies. Biophysical Journal. 98: L60-2. PMID 20550886 DOI: 10.1016/J.Bpj.2010.03.043  0.59
2010 Ulmschneider MB, Doux JP, Killian JA, Smith JC, Ulmschneider JP. Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides. Journal of the American Chemical Society. 132: 3452-60. PMID 20163187 DOI: 10.1021/Ja909347X  0.553
2009 Ulmschneider JP, Doux JP, Killian JA, Smith JC, Ulmschneider MB. Peptide Partitioning and Folding into Lipid Bilayers. Journal of Chemical Theory and Computation. 5: 2202-5. PMID 26616605 DOI: 10.1021/Ct900256K  0.58
2009 Ulmschneider JP, Ulmschneider MB. United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field. Journal of Chemical Theory and Computation. 5: 1803-13. PMID 26610004 DOI: 10.1021/Ct900086B  0.378
2009 Ulmschneider JP, Ulmschneider MB. Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations. Proteins. 75: 586-97. PMID 19003985 DOI: 10.1002/Prot.22270  0.582
2009 Ulmschneider JP. Simulating The Folding And Assembly Of Viral Ion Channels Biophysical Journal. 96: 589a. DOI: 10.1016/J.Bpj.2008.12.3084  0.565
2008 Ulmschneider MB, Ulmschneider JP. Folding Peptides into Lipid Bilayer Membranes. Journal of Chemical Theory and Computation. 4: 1807-9. PMID 26620324 DOI: 10.1021/Ct800100M  0.587
2008 Ulmschneider MB, Ulmschneider JP. Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides. Molecular Membrane Biology. 25: 245-57. PMID 18428040 DOI: 10.1080/09687680802020313  0.592
2007 Ulmschneider JP, Ulmschneider MB. Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model. Journal of Chemical Theory and Computation. 3: 2335-46. PMID 26636223 DOI: 10.1021/Ct700103K  0.523
2007 Ulmschneider JP, Ulmschneider MB, Di Nola A. Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane. Proteins. 69: 297-308. PMID 17600830 DOI: 10.1002/Prot.21519  0.57
2007 Ulmschneider MB, Ulmschneider JP, Sansom MS, Di Nola A. A generalized born implicit-membrane representation compared to experimental insertion free energies. Biophysical Journal. 92: 2338-49. PMID 17218457 DOI: 10.1529/Biophysj.106.081810  0.518
2006 Ulmschneider JP, Ulmschneider MB, Di Nola A. Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations. The Journal of Physical Chemistry. B. 110: 16733-42. PMID 16913813 DOI: 10.1021/Jp061619B  0.426
2004 Ulmschneider JP, Jorgensen WL. Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation. Journal of the American Chemical Society. 126: 1849-57. PMID 14871118 DOI: 10.1021/Ja0378862  0.534
2004 Jorgensen WL, Ulmschneider JP, Tirado-Rives J. Free energies of hydration from a generalized born model and an all-atom force field Journal of Physical Chemistry B. 108: 16264-16270. DOI: 10.1021/Jp0484579  0.404
2004 Ulmschneider JP, Jorgensen WL. Monte Carlo backbone sampling for nucleic acids using concerted rotations including variable bond angles Journal of Physical Chemistry B. 108: 16883-16892. DOI: 10.1021/Jp047796Z  0.48
2003 Ulmschneider JP, Jorgensen WL. Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias Journal of Chemical Physics. 118: 4261-4271. DOI: 10.1063/1.1542611  0.517
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