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1

Are Current Molecular Dynamics Force Fields too Helical?

Best, Robert B., Buchete, Nicolae-Viorel, Hummer, Gerhard

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 392 KB

english, 2008

2

Dynamics of protein folding: Probing the kinetic network of folding–unfolding transitions with experiment and theory

Ginka S. Buchner, Ronan D. Murphy, Nicolae-Viorel Buchete, Jan Kubelka

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2011

Language:

english

File:

PDF, 988 KB

english, 2011

3

Book Review:The Art of Molecular Dynamics Simulation

Nicolae-Viorel Buchete

Journal:

Journal of Statistical Physics

Year:

2005

Language:

english

File:

PDF, 43 KB

english, 2005

4

Santosh K. Upadhyay. Chemical

Nicolae-Viorel Buchete

Journal:

Journal of Statistical Physics

Year:

2007

Language:

english

File:

PDF, 83 KB

english, 2007

5

Orientational potentials extracted from protein structures improve native fold recognition

Nicolae-Viorel Buchete, John E. Straub, Devarajan Thirumalai

Journal:

Protein Science

Year:

2004

Language:

english

File:

PDF, 359 KB

english, 2004

6

Conformational dynamics of human IAPP monomers

Ronan D. Murphy, Jennifer Conlon, Tayyaub Mansoor, Sorin Luca, Sara M. Vaiana, Nicolae-Viorel Buchete

Journal:

Biophysical Chemistry

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

7

Molecular Dynamics Simulations of Alzheimer's β-Amyloid Protofilaments

Nicolae-Viorel Buchete, Robert Tycko, Gerhard Hummer

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 1.13 MB

english, 2005

8

Molecular Interactions of Alzheimer's Aβ Protofilaments with Lipid Membranes

Florentina Tofoleanu, Nicolae-Viorel Buchete

Journal:

Journal of Molecular Biology

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

9

Unlocking the Atomic-Level Details of Amyloid Fibril Growth through Advanced Biomolecular Simulations

Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 57 KB

english, 2012

10

Structure and Dynamics of Parallel β-Sheets, Hydrophobic Core, and Loops in Alzheimer’s Aβ Fibrils

Buchete, Nicolae-Viorel, Hummer, Gerhard

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 918 KB

english, 2007

11

Are Peptides Good Two-State Folders?

Berezhkovskii, Alexander M., Tofoleanu, Florentina, Buchete, Nicolae-Viorel

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.26 MB

english, 2011

12

Conformational and Dynamic Properties of Extracellular Domains of Cell Adhesion Molecules

Kelly, Catherine M., Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 63 KB

english, 2014

13

Probing the Kinetic Network of Folding-Unfolding Transitions in Proteins

Murphy, Ronan D., Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 55 KB

english, 2011

14

Dynamics of Intra- and Inter-Helix Contact Formation

Murphy, Ronan D., Leahy, Cathal, Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 90 KB

english, 2009

15

Molecular Interactions of Alzheimer's Aβ Peptide Fibrils and Oligomers with Lipid Membranes

Tofoleanu, Florentina, Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 37 KB

english, 2013

16

Peptide folding kinetics from replica exchange molecular dynamics

Buchete, Nicolae-Viorel, Hummer, Gerhard

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 245 KB

english, 2008

17

Coarse Master Equations for Peptide Folding Dynamics †

Buchete, Nicolae-Viorel, Hummer, Gerhard

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 518 KB

english, 2008

18

Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations

Rosta, Edina, Buchete, Nicolae-Viorel, Hummer, Gerhard

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 638 KB

english, 2009

19

Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field

Kelly, Catherine M., Northey, Thomas, Ryan, Kate, Brooks, Bernard R., Kholkin, Andrei L., Rodriguez, Brian J., Buchete, Nicolae-Viorel

Journal:

Biophysical Chemistry

Year:

2015

Language:

english

File:

PDF, 2.16 MB

english, 2015

20

Mean First-Passage Time Calculations for the Coil-to-Helix Transition: The Active Helix Ising Model †

Buchete, Nicolae-Viorel, Straub, John E.

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 202 KB

english, 2001

21

Note: Network random walk model of two-state protein folding: Test of the theory

Berezhkovskii, Alexander M., Murphy, Ronan D., Buchete, Nicolae-Viorel

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 299 KB

english, 2013

22

Modulation of Alzheimer’s Aβ Protofilament-Membrane Interactions by Lipid Headgroups

Tofoleanu, Florentina, Brooks, Bernard R., Buchete, Nicolae-Viorel

Journal:

ACS Chemical Neuroscience

Year:

2015

Language:

english

File:

PDF, 3.72 MB

english, 2015

23

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

Nasica-Labouze, Jessica, Nguyen, Phuong H., Sterpone, Fabio, Berthoumieu, Olivia, Buchete, Nicolae-Viorel, Coté, Sébastien, De Simone, Alfonso, Doig, Andrew J., Faller, Peter, Garcia, Angel, Laio, Ale

Journal:

Chemical Reviews

Year:

2015

Language:

english

File:

PDF, 21.73 MB

english, 2015

24

Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules

Kelly, Catherine M., Muzard, Julien, Brooks, Bernard R., Lee, Gil U., Buchete, Nicolae-Viorel

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 4.01 MB

english, 2015

25

Nanoscale Piezoelectric Properties of Self-Assembled Fmoc–FF Peptide Fibrous Networks

Ryan, Kate, Beirne, Jason, Redmond, Gareth, Kilpatrick, Jason I., Guyonnet, Jill, Buchete, Nicolae-Viorel, Kholkin, Andrei L., Rodriguez, Brian J.

Journal:

ACS Applied Materials & Interfaces

Year:

2015

Language:

english

File:

PDF, 938 KB

english, 2015

26

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Par

Journal:

Journal of Membrane Biology

Year:

2015

Language:

english

File:

PDF, 3.91 MB

english, 2015

27

Alzheimer Aβ peptide interactions with lipid membranes

Tofoleanu, Florentina, Buchete, Nicolae-Viorel

Journal:

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

28

Exposure of chick embryos to cadmium changes the extra-embryonic vascular branching pattern and alters expression of VEGF-A and VEGF-R2

Gheorghescu, Anna Kaskova, Tywoniuk, Bartlomiej, Duess, Johannes, Buchete, Nicolae-Viorel, Thompson, Jennifer

Journal:

Toxicology and Applied Pharmacology

Year:

2015

Language:

english

File:

PDF, 1.36 MB

english, 2015

29

Coarse Master Equation-Based Analysis of N-Methylation and Temperature Effects on the Dynamics of Cyclic Peptides

Crowe, Aoife, Sánchez-Sanz, Goar, Tywoniuk, Bartlomiej, Shields, Denis C., Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 43 KB

english, 2016

30

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

Jambrina, Pablo G., Rauch, Nora, Pilkington, Ruth, Rybakova, Katja, Nguyen, Lan K., Kholodenko, Boris N., Buchete, Nicolae-Viorel, Kolch, Walter, Rosta, Edina

Journal:

Angewandte Chemie International Edition

Year:

2016

Language:

english

File:

PDF, 3.29 MB

english, 2016

31

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation

Jambrina, Pablo G., Rauch, Nora, Pilkington, Ruth, Rybakova, Katja, Nguyen, Lan K., Kholodenko, Boris N., Buchete, Nicolae-Viorel, Kolch, Walter, Rosta, Edina

Journal:

Angewandte Chemie

Year:

2016

Language:

english

File:

PDF, 3.26 MB

english, 2016

32

Structural Stability of Diabetes-Related Amylin Protofilaments: Applications to Fibril Design

Yuan, Ye, Tywoniuk, Bartlomiej, Buchete, Nicolae-Viorel

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

33

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers

Leahy, Cathal T., Murphy, Ronan D., Hummer, Gerhard, Rosta, Edina, Buchete, Nicolae-Viorel

Journal:

The Journal of Physical Chemistry Letters

Year:

2016

Language:

english

File:

PDF, 938 KB

english, 2016

34

Thermal and aqueous stability improvement of graphene oxide enhanced diphenylalanine nanocomposites

Ryan, Kate, Neumayer, Sabine M., Maraka, Harsha Vardhan R., Buchete, Nicolae-Viorel, Kholkin, Andrei L., Rice, James H., Rodriguez, Brian J.

Journal:

Science and Technology of Advanced Materials

Year:

2017

Language:

english

File:

PDF, 1.45 MB

english, 2017

35

Variational Identification of Markovian Transition States

Martini, Linda, Kells, Adam, Covino, Roberto, Hummer, Gerhard, Buchete, Nicolae-Viorel, Rosta, Edina

Journal:

Physical Review X

Year:

2017

Language:

english

File:

PDF, 1.87 MB

english, 2017

36

Peptide dimerization-dissociation rates from replica exchange molecular dynamics

Leahy, Cathal T., Kells, Adam, Hummer, Gerhard, Buchete, Nicolae-Viorel, Rosta, Edina

Journal:

The Journal of Chemical Physics

Year:

2017

Language:

english

File:

PDF, 3.30 MB

english, 2017

37

Structural Modulation of Human Amylin Protofilaments by Naturally-Occurring Mutations

Tofoleanu, Florentina, Yuan, Ye, Pickard, Frank C, Tywoniuk, Bartlomiej, Brooks, Bernard R., Buchete, Nicolae-Viorel

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 3.76 MB

english, 2018

38

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions

Sánchez-Sanz, Goar, Tywoniuk, Bartłomiej, Matallanas, David, Romano, David, Nguyen, Lan K., Kholodenko, Boris N., Rosta, Edina, Kolch, Walter, Buchete, Nicolae-Viorel, Keskin, Ozlem

Journal:

PLoS Computational Biology

Year:

2016

Language:

english

File:

PDF, 2.62 MB

english, 2016

39

Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides

Narayan, Brajesh, Herbert, Colm, Yuan, Ye, Rodriguez, Brian J., Brooks, Bernard R., Buchete, Nicolae-Viorel

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.58 MB

english, 2018

40

Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer’s Aβ Protofilaments

Tywoniuk, Bartlomiej, Yuan, Ye, McCartan, Sarah, Szydlowska, Beata Maria, Tofoleanu, Florentina, Brooks, Bernard R., Buchete, Nicolae-Viorel

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 9.51 MB

english, 2018

41

The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning

Narayan, Brajesh, Fathizadeh, Arman, Templeton, Clark, He, Peng, Arasteh, Shima, Elber, Ron, Buchete, Nicolae-Viorel, Levy, Ron M.

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2019

File:

PDF, 2.21 MB

2019

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