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1

Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA

Horenko, Illia, Dittmer, Evelyn, Lankas, Filip, Maddocks, John, Metzner, Philipp, Schütte, Christof

Journal:

SIAM Journal on Applied Dynamical Systems

Year:

2008

Language:

english

File:

PDF, 28.48 MB

english, 2008

2

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

Kamila Réblová, Filip Lankas̆, Filip Rázga, Maryna V. Krasovska, Jaroslav Koc̆a, Jir̆í S̆poner

Journal:

Year:

2006

Language:

english

File:

PDF, 1.50 MB

english, 2006

3

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs

Sklenovský, Petr, Florová, Petra, Banáš, Pavel, Réblová, Kamila, Lankaš, Filip, Otyepka, Michal, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 7.83 MB

english, 2011

4

[IEEE 2010 International Conference on Networking and Information Technology (ICNIT 2010) - Manila, Philippines (2010.06.11-2010.06.12)] 2010 International Conference on Networking and Information Technology - Binding of QSY 21 nonfluorescent quencher to DNA: Structure and dynamics

Kabelac, Martin, Lankas, Filip, Zimandl, Filip, Fessl, Tomas

Year:

2010

Language:

english

File:

PDF, 643 KB

english, 2010

5

rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif

Dršata, Tomáš, Réblová, Kamila, Beššeová, Ivana, Šponer, Jiří, Lankaš, Filip

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1.42 MB

english, 2017

6

Effect of 8-Oxoguanine on DNA Structure and Deformability

Dršata, Tomáš, Kara, Mahmut, Zacharias, Martin, Lankaš, Filip

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.32 MB

english, 2013

7

DNA Deformability at the Base Pair Level

Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E.

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 25 KB

english, 2004

8

Structure, Dynamics, and Interactions of a C4′-Oxidized Abasic Site in DNA: A Concomitant Strand Scission Reverses Affinities

Patel, Chandan, Dršata, Tomàš, Lankaš, Filip, Dumont, Elise

Journal:

Year:

2013

Language:

english

File:

PDF, 1.90 MB

english, 2013

9

Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles

Filip Lankaš, Richard Lavery, John H. Maddocks

Journal:

Year:

2006

Language:

english

File:

PDF, 614 KB

english, 2006

10

Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine

Zelený, Tomáš, Ruckenbauer, Matthias, Aquino, Adelia J.A., Müller, Thomas, Lankaš, Filip, Dršata, Tomáš, Hase, William L., Nachtigallova, Dana, Lischka, Hans

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 3.05 MB

english, 2012

11

Mechanical Model of DNA Allostery

Dršata, Tomáš, Zgarbová, Marie, Špačková, Naďa, Jurečka, Petr, Šponer, Jiří, Lankaš, Filip

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 698 KB

english, 2014

12

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

Lankaš, Filip, Šponer, Jiří, Langowski, Jörg, Cheatham, Thomas E.

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 167 KB

english, 2003

13

Critical Effect of the N2 Amino Group on Structure, Dynamics, and Elasticity of DNA Polypurine Tracts

Lankaš, Filip, Cheatham, Thomas E., Špačáková, Nad’a, Hobza, Pavel, Langowski, Jörg, Šponer, Jiří

Journal:

Biophysical Journal

Year:

2002

Language:

english

File:

PDF, 249 KB

english, 2002

14

Relative Flexibility of DNA and RNA: a Molecular Dynamics Study

Agnes Noy, Alberto Pérez, Filip Lankas, F. Javier Luque, Modesto Orozco

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 595 KB

english, 2004

15

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

Banáš, Pavel, Mládek, Arnošt, Otyepka, Michal, Zgarbová, Marie, Jurečka, Petr, Svozil, Daniel, Lankaš, Filip, Šponer, Jiří

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 4.17 MB

english, 2012

16

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

Zgarbová, Marie, Otyepka, Michal, Šponer, Jiří, Lankaš, Filip, Jurečka, Petr

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 4.08 MB

english, 2014

17

Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation

Dohnalova, Hana, Drsata, Tomas, Sponer, Jiri, Zacharias, Martin, Lipfert, Jan, Lankas, Filip

Journal:

Journal of Chemical Theory and Computation

Year:

2020

Language:

english

File:

PDF, 504 KB

english, 2020

18

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps

Beveridge, David L., Barreiro, Gabriela, Suzie Byun, K., Case, David A., Cheatham, Thomas E., Dixit, Surjit B., Giudice, Emmanuel, Lankas, Filip, Lavery, Richard, Maddocks, John H., Osman, Roman, Seib

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 346 KB

english, 2004

19

Sequence-dependent elastic properties of DNA

Filip Lankaš, Jiřı́ Šponer, Pavel Hobza, Jörg Langowski

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 295 KB

english, 2000

20

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

Dršata, Tomáš, Pérez, Alberto, Orozco, Modesto, Morozov, Alexandre V., Šponer, Jiří, Lankaš, Filip

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.03 MB

english, 2013

21

Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution

Špačková, Nad'a, Cheatham, Thomas E., Ryjáček, Filip, Lankaš, Filip, van Meervelt, Luc, Hobza, Pavel, Šponer, Jiří

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 335 KB

english, 2003

22

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

Dršata, Tomáš, Zgarbová, Marie, Jurečka, Petr, Šponer, Jiří, Lankaš, Filip

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 166 KB

english, 2016

23

Impact of the nucleosome histone core on the structure and dynamics of DNA containing pyrimidine-pyrimidone (6-4) photoproduct

Matouskova, Eva, Bignon, Emmanuelle, Claerbout, Victor E.P., Drsata, Tomas, Gillet, Natacha, Monari, Antonio, Dumont, Elise, Lankas, Filip

Journal:

Journal of Chemical Theory and Computation

Year:

2020

File:

PDF, 1.09 MB

2020

24

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps

Dixit, Surjit B., Beveridge, David L., Case, David A., Cheatham, Thomas E., Giudice, Emmanuel, Lankas, Filip, Lavery, Richard, Maddocks, John H., Osman, Roman, Sklenar, Heinz, Thayer, Kelly M., Varnai

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 780 KB

english, 2005

25

Sequence-Dependent Twist-Stretch Coupling in DNA

Lionnet, Timothée, Lankaš, Filip

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 1.83 MB

english, 2007

26

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences

Zgarbová, Marie, Jurečka, Petr, Lankaš, Filip, Cheatham, Thomas E., Šponer, Jiří, Otyepka, Michal

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 3.11 MB

english, 2017

27

The temperature dependence of the helical twist of DNA

Kriegel, Franziska, Matek, Christian, Dršata, Tomáš, Kulenkampff, Klara, Tschirpke, Sophie, Zacharias, Martin, Lankaš, Filip, Lipfert, Jan

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 1.60 MB

english, 2018

28

Insights into the Structure of Intrastrand Cross-Link DNA Lesion-Containing Oligonucleotides: G[8–5m]T and G[8–5]C from Molecular Dynamics Simulations

Dumont, Elise, Dršata, Tomáš, Guerra, Célia Fonseca, Lankaš, Filip

Journal:

Year:

2015

Language:

english

File:

PDF, 3.45 MB

english, 2015

29

Theoretical models of DNA flexibility

Dršata, Tomáš, Lankaš, Filip

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2013

Language:

english

File:

PDF, 257 KB

english, 2013

30

Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics

Bignon, Emmanuelle, Dršata, Tomáš, Morell, Christophe, Lankaš, Filip, Dumont, Elise

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.21 MB

english, 2016

31

DNA sequence-dependent deformability—insights from computer simulations

Journal:

Year:

2004

Language:

english

File:

PDF, 250 KB

english, 2004

32

Monte Carlo simulation of chromatin stretching

Aumann, Frank, Lankas, Filip, Caudron, Maïwen, Langowski, Jörg

Journal:

Physical Review E

Year:

2006

Language:

english

File:

PDF, 469 KB

english, 2006

33

Multiscale modelling of DNA mechanics

Dršata, Tomáš, Lankaš, Filip

Journal:

Journal of Physics Condensed Matter

Year:

2015

Language:

english

File:

PDF, 1.09 MB

english, 2015

34

Long-timescale dynamics of the Drew–Dickerson dodecamer

Dans, Pablo D., Danilāne, Linda, Ivani, Ivan, Dršata, Tomáš, Lankaš, Filip, Hospital, Adam, Walther, Jürgen, Pujagut, Ricard Illa, Battistini, Federica, Gelpí, Josep Lluis, Lavery, Richard, Orozco, Mo

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 7.96 MB

english, 2016

35

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis

Liebl, Korbinian, Drsata, Tomas, Lankas, Filip, Lipfert, Jan, Zacharias, Martin

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 7.59 MB

english, 2015

36

Structural and dynamic effects of single 7-hydro-8-oxoguanine bases located in a frameshift target DNA sequence

Flavia Barone, Filip Lankas, Nada Spackova, Jiri Sponer, Peter Karran, Margherita Bignami, Filomena Mazzei

Journal:

Biophysical Chemistry

Year:

2005

Language:

english

File:

PDF, 331 KB

english, 2005

37

[RSC Biomolecular Sciences] Innovations in Biomolecular Modeling and Simulations Volume 2 || Chapter 1. Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale

Year:

2012

Language:

english

File:

PDF, 984 KB

english, 2012

38

A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics

Kabeláč, Martin, Zimandl, Filip, Fessl, Tomáš, Chval, Zdeněk, Lankaš, Filip

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.73 MB

english, 2010

39

Effect O6-guanine alkylation on DNA flexibility studied by comparative molecular dynamics simulations

Kara, Mahmut, Drsata, Tomas, Lankas, Filip, Zacharias, Martin, Case, David A.

Journal:

Year:

2015

Language:

english

File:

PDF, 861 KB

english, 2015

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