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1

Computation of writhe in modeling of supercoiled DNA

Konstantin Klenin, Jörg Langowski

Journal:

Year:

2000

Language:

english

File:

PDF, 192 KB

english, 2000

2

Derivatives of molecular surface area and volume: Simple and exact analytical formulas

Konstantin V. Klenin, Frank Tristram, Timo Strunk, Wolfgang Wenzel

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 519 KB

english, 2011

3

Branched DNA That Forms a Solid at 95 °C

Arunoday Singh, Mariyan Tolev, Martin Meng, Dr. Konstantin Klenin, Oliver Plietzsch, Christine I. Schilling, Dr. Thierry Muller, Dr. Martin Nieger, Prof. Stefan Bräse, Priv.-Doz. Dr. Wolfgang Wenzel,

Journal:

Angewandte Chemie

Year:

2011

Language:

english

File:

PDF, 537 KB

english, 2011

4

Branched DNA That Forms a Solid at 95 °C

Arunoday Singh, Mariyan Tolev, Martin Meng, Dr. Konstantin Klenin, Oliver Plietzsch, Christine I. Schilling, Dr. Thierry Muller, Dr. Martin Nieger, Prof. Stefan Bräse, Priv.-Doz. Dr. Wolfgang Wenzel,

Journal:

Angewandte Chemie International Edition

Year:

2011

Language:

english

File:

PDF, 526 KB

english, 2011

5

Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations

Jörg Langowski, Ulrike Kapp, Konstantin Klenin, Alexander Vologodskii

Journal:

Year:

1994

Language:

english

File:

PDF, 713 KB

english, 1994

6

Modelling proteins: Conformational sampling and reconstruction of folding kinetics

Konstantin Klenin, Birgit Strodel, David J. Wales, Wolfgang Wenzel

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2011

Language:

english

File:

PDF, 1.42 MB

english, 2011

7

Kinetics of antigen binding to antibody microspots: Strong limitation by mass transport to the surface

Wlad Kusnezow, Yana V. Syagailo, Sven Rüffer, Konstantin Klenin, Walter Sebald, Jörg D. Hoheisel, Christoph Gauer, Igor Goychuk

Journal:

Year:

2006

Language:

english

File:

PDF, 356 KB

english, 2006

8

Template-free protein structure prediction and quality assessment with an all-atom free-energy model

Srinivasa Murthy Gopal, Konstantin Klenin, Wolfgang Wenzel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 998 KB

english, 2009

9

Superhelical DNA studied by solution scattering and computer models

Jörg Langowski, Markus Hammermann, Konstantin Klenin, Roland May, Katalin Tóth

Journal:

Year:

1999

Language:

english

File:

PDF, 96 KB

english, 1999

10

Conformational and thermodynamic properties of supercoiled DNA

Alexander V. Vologodskii, Stephen D. Levene, Konstantin V. Klenin, Maxim Frank-Kamenetskii, Nicholas R. Cozzarelli

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 3.04 MB

english, 1992

11

Computational Analysis of the Chiral Action of Type II DNA Topoisomerases

Konstantin Klenin, Jörg Langowski, Alexander Vologodskii

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 316 KB

english, 2002

12

Kinetics of Site–Site Interactions in Supercoiled DNA with Bent Sequences

Malte Bussiek, Konstantin Klenin, Jörg Langowski

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.03 MB

english, 2002

13

Intrachain Reactions of Supercoiled DNA Simulated by Brownian Dynamics

Klenin, Konstantin V., Langowski, Jörg

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 172 KB

english, 2001

14

Diffusion-Controlled Intrachain Reactions of Supercoiled DNA: Brownian Dynamics Simulations

Klenin, Konstantin V., Langowski, Jörg

Journal:

Biophysical Journal

Year:

2001

Language:

english

File:

PDF, 182 KB

english, 2001

15

Computer simulation of DNA supercoiling

Konstantin V. Klenin, Alexander V. Vologodskii, Vadim V. Anshelevich, Alexander M. Dykhne, Maxim D. Frank-Kamenetskii

Journal:

Journal of Molecular Biology

Year:

1991

Language:

english

File:

PDF, 660 KB

english, 1991

16

Performance of An All-Atom Free Energy Approach For Protein Structure Prediction

Anand, Priya, Strunk, Timo, Brieg, Martin, Meliciani, Irene, Wolf, Moritz, Klenin, Konstantin, Wenzel, Wolfgang

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 31 KB

english, 2011

17

Looping Dynamics of Linear DNA Molecules and the Effect of DNA Curvature: A Study by Brownian Dynamics Simulation

Merlitz, Holger, Rippe, Karsten, Klenin, Konstantin V., Langowski, Jörg

Journal:

Biophysical Journal

Year:

1998

Language:

english

File:

PDF, 196 KB

english, 1998

18

A Brownian Dynamics Program for the Simulation of Linear and Circular DNA and Other Wormlike Chain Polyelectrolytes

Klenin, Konstantin, Merlitz, Holger, Langowski, Jörg

Journal:

Biophysical Journal

Year:

1998

Language:

english

File:

PDF, 222 KB

english, 1998

19

Salt-Dependent DNA Superhelix Diameter Studied by Small Angle Neutron Scattering Measurements and Monte Carlo Simulations

Hammermann, Markus, Brun, Nathalie, Klenin, Konstantin V., May, Roland, Tóth, Katalin, Langowski, Jörg

Journal:

Biophysical Journal

Year:

1998

Language:

english

File:

PDF, 129 KB

english, 1998

20

Facilitated Diffusion of DNA-Binding Proteins

Klenin, Konstantin V., Merlitz, Holger, Langowski, Jörg, Wu, Chen-Xu

Journal:

Physical Review Letters

Year:

2006

Language:

english

File:

PDF, 133 KB

english, 2006

21

Probing hot spots on protein-protein interfaces with all-atom free-energy simulation

Meliciani, Irene, Klenin, Konstantin, Strunk, Timo, Schmitz, Katja, Wenzel, Wolfgang

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.31 MB

english, 2009

22

Calculation of the “absolute” free energy of a β-hairpin in an all-atom force field

Klenin, Konstantin V., Wenzel, Wolfgang

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 503 KB

english, 2013

23

All Atom Protein Folding Simulations With Distributed Computational Resources

Strunk, Timo, Klenin, Konstantin, Wenzel, Wolfgang

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 37 KB

english, 2009

24

Kinetics of protein binding in solid-phase immunoassays: Theory

Klenin, Konstantin V., Kusnezow, Wlad, Langowski, Jörg

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 473 KB

english, 2005

25

Modeling Dynamic Light Scattering of Supercoiled DNA

Klenin, Konstantin, Hammermann, Markus, Langowski, Jörg

Journal:

Year:

2000

Language:

english

File:

PDF, 216 KB

english, 2000

26

Efficient calculation of rate constants: Downhill versus uphill sampling

Klenin, Konstantin V.

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 529 KB

english, 2014

27

Modeling of intramolecular reactions of polymers: An efficient method based on Brownian dynamics simulations

Klenin, Konstantin V., Langowski, Jörg

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 390 KB

english, 2004

28

A method for the calculation of rate constants from stochastic transition paths

Klenin, Konstantin V., Wenzel, Wolfgang

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 350 KB

english, 2010

29

Transition network based on equilibrium sampling: A new method for extracting kinetic information from Monte Carlo simulations of protein folding

Klenin, Konstantin V., Wenzel, Wolfgang

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.14 MB

english, 2011

30

Facilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions

Merlitz, Holger, Klenin, Konstantin V., Wu, Chen-Xu, Langowski, Jörg

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 337 KB

english, 2006

31

Kinetics of intrachain reactions of supercoiled DNA: Theory and numerical modeling

Klenin, Konstantin V., Langowski, Jörg

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 469 KB

english, 2001

32

Facilitated diffusion of DNA-binding proteins: Simulation of large systems

Merlitz, Holger, Klenin, Konstantin V., Wu, Chen-Xu, Langowski, Jörg

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 542 KB

english, 2006