Baumketner, Andrij: search on Z-Library

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1

The Thermodynamics of Folding of a β Hairpin Peptide Probed Through Replica Exchange Molecular Dynamics Simulations

Andrij Baumketner, Joan-Emma Shea

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2006

Language:

english

File:

PDF, 505 KB

english, 2006

2

Structure of the 21–30 fragment of amyloid β-protein

Andrij Baumketner, Summer L. Bernstein, Thomas Wyttenbach, Noel D. Lazo, David B. Teplow, Michael T. Bowers, Joan-Emma Shea

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 499 KB

english, 2006

3

Microscopic Factors that Control β-Sheet Registry in Amyloid Fibrils Formed by Fragment 11–25 of Amyloid β Peptide: Insights from Computer Simulations

Lacramioara Negureanu, Andrij Baumketner

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 1.27 MB

english, 2009

4

Electric Field as a Disaggregating Agent for Amyloid Fibrils

Baumketner, Andrij

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 2.06 MB

english, 2014

5

The Influence of Different Treatments of Electrostatic Interactions on the Thermodynamics of Folding of Peptides †

Baumketner, Andrij, Shea, Joan-Emma

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 353 KB

english, 2005

6

Optimized Image Charges for Reaction Field Calculations

Song, Wei, Lin, Yuchun, Baumketner, Andrij, Cai, Wei, Jacobs, Donald J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 33 KB

english, 2011

7

Removing systematic errors in interionic potentials of mean force computed in molecular simulations using reaction-field-based electrostatics

Baumketner, Andrij

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 312 KB

english, 2009

8

An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions

Lin, Yuchun, Baumketner, Andrij, Deng, Shaozhong, Xu, Zhenli, Jacobs, Donald, Cai, Wei

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 853 KB

english, 2009

9

Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics

Boris Ni, Andrij Baumketner

Journal:

Journal of Molecular Modeling

Year:

2011

Language:

english

File:

PDF, 487 KB

english, 2011

10

Amyloid β-Protein: Experiment and Theory on the 21−30 Fragment

Murray, Megan M., Krone, Mary Griffin, Bernstein, Summer L., Baumketner, Andrij, Condron, Margaret M., Lazo, Noel D., Teplow, David B., Wyttenbach, Thomas, Shea, Joan-Emma, Bowers, Michael T.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 534 KB

english, 2009

11

ICSM: An order method for calculating electrostatic interactions added to TINKER

Katherine Baker, Andrij Baumketner, Yuchun Lin, Shaozhong Deng, Donald Jacobs, Wei Cai

Journal:

Computer Physics Communications

Year:

2013

Language:

english

File:

PDF, 521 KB

english, 2013

12

Aggregation of polyalanine in a hydrophobic environment

Soto, Patricia, Baumketner, Andrij, Shea, Joan-Emma

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 734 KB

english, 2006

13

Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations

Andrij Baumketner, Yuri Nesmelov

Journal:

Protein Science

Year:

2011

Language:

english

File:

PDF, 1.27 MB

english, 2011

14

Amyloid β-protein monomer structure: A computational and experimental study

Andrij Baumketner, Summer L. Bernstein, Thomas Wyttenbach, Gal Bitan, David B. Teplow, Michael T. Bowers, Joan-Emma Shea

Journal:

Protein Science

Year:

2006

Language:

english

File:

PDF, 363 KB

english, 2006

15

The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein

Andrij Baumketner

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 658 KB

english, 2012

16

Effects of Familial Alzheimer’s Disease Mutations on the Folding Nucleation of the Amyloid β-Protein

Mary Griffin Krone, Andrij Baumketner, Summer L. Bernstein, Thomas Wyttenbach, Noel D. Lazo, David B. Teplow, Michael T. Bowers, Joan-Emma Shea

Journal:

Journal of Molecular Biology

Year:

2008

Language:

english

File:

PDF, 478 KB

english, 2008

17

A new FFT-based algorithm to compute Born radii in the generalized Born theory of biomolecule solvation

Wei Cai, Zhenli Xu, Andrij Baumketner

Journal:

Journal of Computational Physics

Year:

2008

Language:

english

File:

PDF, 517 KB

english, 2008

18

The Structure of the Alzheimer Amyloid β 10-35 Peptide Probed through Replica-Exchange Molecular Dynamics Simulations in Explicit Solvent

Andrij Baumketner, Joan-Emma Shea

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 620 KB

english, 2007

19

Amyloid β-Protein: Monomer Structure and Early Aggregation States of Aβ42 and Its Pro 19 Alloform

Bernstein, Summer L., Wyttenbach, Thomas, Baumketner, Andrij, Shea, Joan-Emma, Bitan, Gal, Teplow, David B., Bowers, Michael T.

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 178 KB

english, 2005

20

Folding Landscapes of the Alzheimer Amyloid-β(12-28) Peptide

Andrij Baumketner, Joan-Emma Shea

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 954 KB

english, 2006

21

Ionic solvation studied by image-charge reaction field method

Lin, Yuchun, Baumketner, Andrij, Song, Wei, Deng, Shaozhong, Jacobs, Donald, Cai, Wei

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 497 KB

english, 2011

22

Elucidating Amyloid β-Protein Folding and Assembly: A Multidisciplinary Approach

Teplow, David B., Lazo, Noel D., Bitan, Gal, Bernstein, Summer, Wyttenbach, Thomas, Bowers, Michael T., Baumketner, Andrij, Shea, Joan-Emma, Urbanc, Brigita, Cruz, Luis, Borreguero, Jose, Stanley, H.

Journal:

Accounts of Chemical Research

Year:

2006

Language:

english

File:

PDF, 494 KB

english, 2006

23

Interactions between relay helix and Src homology 1 (SH1) domain helix drive the converter domain rotation during the recovery stroke of myosin II

Andrij Baumketner

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.34 MB

english, 2012

24

Reduced atomic pair-interaction design (RAPID) model for simulations of proteins

Ni, Boris, Baumketner, Andrij

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 4.54 MB

english, 2013

25

Stability of a protein tethered to a surface

Friedel, Miriam, Baumketner, Andrij, Shea, Joan-Emma

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 279 KB

english, 2007

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