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1

Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field

Jorgensen, William L., Ulmschneider, Jakob P., Tirado-Rives, Julian

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 115 KB

english, 2004

2

Mechanisms of molecular transport through the urea channel of Helicobacter pylori

McNulty, Reginald, Ulmschneider, Jakob P., Luecke, Hartmut, Ulmschneider, Martin B.

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 3.05 MB

english, 2013

3

Insights from Micro-second Atomistic Simulations of Melittin in Thin Lipid Bilayers

Upadhyay, Sanjay K., Wang, Yukun, Zhao, Tangzhen, Ulmschneider, Jakob P.

Journal:

Journal of Membrane Biology

Year:

2015

Language:

english

File:

PDF, 3.29 MB

english, 2015

4

Monte carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane

Jakob P. Ulmschneider, Martin B. Ulmschneider, Alfredo Di Nola

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.15 MB

english, 2007

5

Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations

Jakob P. Ulmschneider, Martin B. Ulmschneider

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 708 KB

english, 2009

6

Determining Peptide Partitioning Properties via Computer Simulation

Jakob P. Ulmschneider, Magnus Andersson, Martin B. Ulmschneider

Journal:

Journal of Membrane Biology

Year:

2011

Language:

english

File:

PDF, 1.34 MB

english, 2011

7

Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias

Jorgensen, William L., Ulmschneider, Jakob P.

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 587 KB

english, 2003

8

Peptide Partitioning Properties from Direct Insertion Studies

Ulmschneider, Martin B., Smith, Jeremy C., Ulmschneider, Jakob P.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 725 KB

english, 2010

9

Reorientation and Dimerization of the Membrane-Bound Antimicrobial Peptide PGLa from Microsecond All-Atom MD Simulations

Ulmschneider, Jakob P., Smith, Jeremy C., Ulmschneider, Martin B., Ulrich, Anne S., Strandberg, Erik

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 2.40 MB

english, 2012

10

A Generalized Born Implicit-Membrane Representation Compared to Experimental Insertion Free Energies

Ulmschneider, Martin B., Ulmschneider, Jakob P., Sansom, Mark S.P., Di Nola, Alfredo

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 908 KB

english, 2007

11

Conformational States of Melittin at a Bilayer Interface

Andersson, Magnus, Ulmschneider, Jakob P., Ulmschneider, Martin B., White, Stephen H.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 474 KB

english, 2013

12

Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides

Ulmschneider, Martin B., Ulmschneider, Jakob P.

Journal:

Molecular Membrame Biology

Year:

2008

Language:

english

File:

PDF, 755 KB

english, 2008

13

In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides under Equilibrium Conditions

Ulmschneider, Jakob P., Smith, Jeremy C., White, Stephen H., Ulmschneider, Martin B.

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 4.22 MB

english, 2011

14

How reliable are molecular dynamics simulations of membrane active antimicrobial peptides?

Wang, Yukun, Zhao, Tangzheng, Wei, Dongqing, Strandberg, Erik, Ulrich, Anne S., Ulmschneider, Jakob P.

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2014

Language:

english

File:

PDF, 1.99 MB

english, 2014

15

Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding Simulations

Ulmschneider, Jakob P., Ulmschneider, Martin B., Di Nola, Alfredo

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 420 KB

english, 2006

16

Short Stories - on Antimicrobial Peptides that are Too Short to Span the Membrane

Ulrich, Anne S., Heidenreich, Nico, Wadhwani, Parvesh, Reichert, Johannes, Strandberg, Erik, Misievicz, Julia, Afonin, Sergii, Berditsch, Marina, Bürck, Jochen, Tiltak, Deniz, Ulmschneider, Jakob, Ben

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 72 KB

english, 2012

17

Microsecond Molecular Dynamics Simulations of the Open State Structure of a Bacterial Voltage-Gated Sodium Channel Reveal Mechanisms of Ion Selectivity and Conduction

Ulmschneider, Martin B., Bagnéris, Claire, McCusker, Emily C., Ulmschneider, Jakob P., Wallace, B.A.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 96 KB

english, 2013

18

Simulating The Folding And Assembly Of Viral Ion Channels

Ulmschneider, Jakob P.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 74 KB

english, 2009

19

INTERNATIONAL CONGRESS OF MEDICINE, PARIS, AUGUST, 1900.

Ulmschneider, Jakob P.

Journal:

Year:

1900

Language:

english

File:

PDF, 185 KB

english, 1900

20

Adsorption and Insertion Kinetics of Membrane Active Peptides from Fully Atomistic Simulations

Ulmschneider, Jakob P.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 67 KB

english, 2011

21

The Difference Between Translocon-Assisted Membrane Insertion and Free Surface-To-Bilayer Peptide Insertion

Ulmschneider, Jakob P., White, Stephen H., Smith, Jeremy, Ulmschneider, Martin B.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 74 KB

english, 2012

22

Membrane Translocation of Highly Charged Antimicrobial Peptides via Multi-Microsecond All-Atom Md Simulations

Ulmschneider, Jakob P., Wang, Yukun

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 120 KB

english, 2014

23

Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides

Ulmschneider, Martin B., Doux, Jacques P. F., Killian, J. Antoinette, Smith, Jeremy C., Ulmschneider, Jakob P.

Journal:

Journal of the American Chemical Society

Year:

2010

Language:

english

File:

PDF, 4.84 MB

english, 2010

24

Peptide Partitioning and Folding into Lipid Bilayers

Ulmschneider, Jakob P., Doux, Jacques P. F., Killian, J. Antoinette, Smith, Jeremy C., Ulmschneider, Martin B.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 3.10 MB

english, 2009

25

Monte Carlo Backbone Sampling for Nucleic Acids Using Concerted Rotations Including Variable Bond Angles

Ulmschneider, Jakob P., Jorgensen, William L.

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 487 KB

english, 2004

26

United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field

Ulmschneider, Jakob P., Ulmschneider, Martin B.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 3.66 MB

english, 2009

27

Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model

Ulmschneider, Jakob P., Ulmschneider, Martin B.

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 393 KB

english, 2007

28

Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation

Ulmschneider, Jakob P., Jorgensen, William L.

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 356 KB

english, 2004

29

Folding Peptides into Lipid Bilayer Membranes

Ulmschneider, Martin B., Ulmschneider, Jakob P.

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 749 KB

english, 2008

30

Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion

Ulmschneider, Martin B., Ulmschneider, Jakob P., Schiller, Nina, Wallace, B. A., von Heijne, Gunnar, White, Stephen H.

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 3.63 MB

english, 2014

31

Applications of rare event dynamics on the free energy calculations for membrane protein systems

Wang, Yun-Kun, Wei, Dong-Qing, Gu, Ruo-Xu, Fan, Huai-Meng, Ulmschneider, Jakob

Journal:

Canadian Journal of Chemistry

Year:

2013

Language:

english

File:

PDF, 1.54 MB

english, 2013

32

How Reliable are Molecular Dynamics Simulations of Membrane Active Antimicrobial Peptides

Wang, Yukun, Ulmschneider, Jakob P, Zhao, Shidi

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 41 KB

english, 2015

33

Molecular Dynamics Simulations of the Open State Structure of a Bacterial Voltage-Gated Sodium Channel Reveal the Binding Mechanisms of Channel Blockers

Ke, Song, Wallace, B. Ann, Ulmschneider, Jakob P., Ulmschneider, Martin B.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 45 KB

english, 2016

34

Dynamics of Gal80p in the Gal80p-Gal3p Complex Differ Significantly from the Dynamics in the Gal80p-Gal1p Complex: Implications for the Higher Specificity of Gal3p Towards Transcriptional Induction of Gal Genes

Upadhyay, Sanjay K., Ulmschneider, Jakob P.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 56 KB

english, 2015

35

Insights from Microsecond Atomistic Simulations of Melittin in thin Lipid Bilayers

Ulmschneider, Jakob P., Upadhyay, Sanjay K.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 37 KB

english, 2016

36

ChemInform Abstract: Applications of Rare Event Dynamics on the Free Energy Calculations for Membrane Protein Systems

Wang, Yun-Kun, Wei, Dong-Qing, Gu, Ruo-Xu, Fan, Huai-Meng, Ulmschneider, Jakob

Journal:

Year:

2013

File:

PDF, 20 KB

2013

37

Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

Wang, Yukun, Chen, Charles H., Hu, Dan, Ulmschneider, Martin B., Ulmschneider, Jakob P.

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 7.88 MB

english, 2016

38

Spontaneous Formation of an Ensemble of Structurally Diverse Membrane Channel Architectures from a Single Antimicrobial Peptide Maculatin

Wang, Yukun, Chen, Charles, Hu, Dan, Ulmschneider, Jakob, Ulmschneider, Martin

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 49 KB

english, 2017

39

Insertion Process of Different Amphipathic α-Helical AMPS into Lipid Bilayers Observed in Unbiased Atomic Molecular Dynamics Simulations

Zhao, Tangzhen, Wang, Yukun, Hu, Dan, Ulmschneider, Jakob

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

40

Simulation and Database-Guided Antimicrobial Peptide Evolution

Chen, Charles H., Starr, Charles G., Wiedman, Gregory, Wimley, William C., Ulmschneider, Jakob P., Ulmschneider, Martin B.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

41

How Antimicrobial Peptides Permeabilize Membranes with and without Pore Formation

Ulmschneider, Jakob P.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 47 KB

english, 2017

42

How C-Terminal Domain Stabilize the Gate of Voltage-Gated Sodium Channels

Ke, Song, Ann Wallace, Bonnie, Ulmschneider, Jakob, Ulmschneider, Martin

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

43

Transmembrane helices containing a charged arginine are thermodynamically stable

Ulmschneider, Martin B., Ulmschneider, Jakob P., Freites, J. Alfredo, von Heijne, Gunnar, Tobias, Douglas J., White, Stephen H.

Journal:

European Biophysics Journal

Year:

2017

Language:

english

File:

PDF, 1.81 MB

english, 2017

44

Ab-Initio Prediction of Antimicrobial Peptides Channels in Membranes

Ulmschneider, Jakob

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 44 KB

english, 2018

45

Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

Gumbart, James C., Ulmschneider, Martin B., Hazel, Anthony, White, Stephen H., Ulmschneider, Jakob P.

Journal:

Journal of Membrane Biology

Year:

2018

Language:

english

File:

PDF, 4.96 MB

english, 2018

46

Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes

Ulmschneider, Jakob P., Ulmschneider, Martin B.

Journal:

Accounts of Chemical Research

Year:

2018

Language:

english

File:

PDF, 2.72 MB

english, 2018

47

Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

Gumbart, James C., Ulmschneider, Martin B., Hazel, Anthony, White, Stephen H., Ulmschneider, Jakob P.

Journal:

Journal of Membrane Biology

Year:

2018

Language:

english

File:

PDF, 514 KB

english, 2018

48

The importance of the membrane interface as the reference state for membrane protein stability

Ulmschneider, Jakob P., Smith, Jeremy C., White, Stephen H., Ulmschneider, Martin B.

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2018

Language:

english

File:

PDF, 2.64 MB

english, 2018

49

Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel

Ke, Song, Ulmschneider, Martin B., Wallace, B.A., Ulmschneider, Jakob P.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 4.16 MB

english, 2018

50

Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly

Chen, Charles H, Melo, Marcelo CR, Berglund, Nils, Khan, Ayesha, de la Fuente, CÃ©sar, Ulmschneider, Jakob P, Ulmschneider, Martin B

Journal:

Current Opinion in Structural Biology

Year:

2020

Language:

english

File:

PDF, 1.11 MB

english, 2020

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