Computational studies of RNA and DNA:
Saved in:
| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Dordrecht
Springer
2006
|
| Series: | Challenges and Advances in Computational Chemistry and Physics
2 |
| Subjects: | |
| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XI, 636 S. Ill., graph. Darst. |
| ISBN: | 1402047940 9781402047947 |
Staff View
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| adam_text | CONTENTS
Preface ix
1. Basics ofNucleic Acid Structure
Bohdan Schneider and Helen M. Berman 1
2. Using Amber to Simulate DNA and RNA
Thomas E. Cheatham, III and David A. Case 45
3. Theoretical Studies ofNucleic Acids and Nucleic
Acid Protein Complexes using Charmm
Alexander D. MacKerell, Jr. andLennart Nilsson 73
4. Continuum Solvent Models to Study the Structure
and Dynamics ofNucleic Acids and Complexes with Ligands
Martin Zacharias 95
5. Data Mining of Molecular Dynamic Trajectories
ofNucleic Acids
Modesto Orozco, Agnes Noy, Tim Meyer, Manuel Rueda,
Carles Ferrer, Antonio Valencia, Alberto Perez,
Oliver Carrillo, Juan Fernandez Recio, Xavier de la Cruz
and F. Javier Luque 121
6. Enhanced Sampling Methods for Atomistic Simulation
ofNucleic Acids
Catherine Kelso and Carlos Simmerling 147
7. Modeling DNA Deformation
Peter Värnai and Richard Lavery 169
8. Molecular Dynamics Simulations and Free Energy
Calculations on Protein Nucleic Acid Complexes
David L. Beveridge, Surjit B. Dixit, Bethany L. Kormos
Anne M. Baranger and B. Jayaram 211
V
vi Contents
9. DNA Simulation Benchmarks as Revealed
by X Ray Structures
Wilma K. Olson, Andrew V. Colasanti, Yun Li, Wei Ge,
Guohui Zheng, and Victor B. Zhurkin 235
10. RNA:The Cousin Left Behind Becomes a Star
Tamar Schlick 259
11. Molecular Dynamics Simulations of RNA Systems:
Importance of the Initial Conditions
Pascal Auffinger 283
12. Molecular Dynamics Simulations of Nucleic Acids
Nad a Spackovä, Thomas E. Cheatham, III and Jifi Sponer 301
13. Using Computer Simulations to Study Decoding
by the Ribosome
Kevin Y. Sanbonmatsu 327
14. Base Stacking and Base Pairing
Jifi Sponer, Petr Jurecka and Pavel Hobza 343
15. Interaction of Metal Cations with Nucleic Acids
and their Building Units
Judit E. Sponer, Jaroslav V. Burda, Jerzy Leszczynki,
and Jifi Sponer 389
16. Proton Transfer in DNA Base Pairs
J. Bertran, L. Biancafort, M. Noguera, M. Sodupe 411
17. Comparative Study of Quantum Mechanical Methods
Related to Nucleic Acid Bases: Electronic Spectra, Excited
State Structures and Interactions
M.K. Shukla and Jerzy Leszczynski 433
18. Substituent Effects on Hydrogen Bonds in DNA
Celia Fonseca Guerra and F. Matthias Bickelhaupt 463
19. Computational modeling of Charge Transfer in DNA
Alexander A. Voityuk 485
20. Quantum Chemical Calculations of NMR Parameters
Wolfgang Schöfberger, Vladimir Sychrovsky and
Lukas Trantirek 513
Contents vii
21. The Importance of Entropie Factors in DNA Behaviour:
Insights from Simulations
Sarah A. Harris and Charles A. Laughton 537
22. Sequence Dependent Harmonie Deformability of Nucleic
Acids Inferred from Atomistic Molecular Dynamics
Filip Lankas 559
23. Simulation of Equilibrium and Dynamic Properties
of Large DNA Molecules
Alexander Vologodskii 579
24. Chromatin Simulations
J. Langowski and H. Schiessel 605
Index 635
|
| adam_txt |
CONTENTS
Preface ix
1. Basics ofNucleic Acid Structure
Bohdan Schneider and Helen M. Berman 1
2. Using Amber to Simulate DNA and RNA
Thomas E. Cheatham, III and David A. Case 45
3. Theoretical Studies ofNucleic Acids and Nucleic
Acid Protein Complexes using Charmm
Alexander D. MacKerell, Jr. andLennart Nilsson 73
4. Continuum Solvent Models to Study the Structure
and Dynamics ofNucleic Acids and Complexes with Ligands
Martin Zacharias 95
5. Data Mining of Molecular Dynamic Trajectories
ofNucleic Acids
Modesto Orozco, Agnes Noy, Tim Meyer, Manuel Rueda,
Carles Ferrer, Antonio Valencia, Alberto Perez,
Oliver Carrillo, Juan Fernandez Recio, Xavier de la Cruz
and F. Javier Luque 121
6. Enhanced Sampling Methods for Atomistic Simulation
ofNucleic Acids
Catherine Kelso and Carlos Simmerling 147
7. Modeling DNA Deformation
Peter Värnai and Richard Lavery 169
8. Molecular Dynamics Simulations and Free Energy
Calculations on Protein Nucleic Acid Complexes
David L. Beveridge, Surjit B. Dixit, Bethany L. Kormos
Anne M. Baranger and B. Jayaram 211
V
vi Contents
9. DNA Simulation Benchmarks as Revealed
by X Ray Structures
Wilma K. Olson, Andrew V. Colasanti, Yun Li, Wei Ge,
Guohui Zheng, and Victor B. Zhurkin 235
10. RNA:The Cousin Left Behind Becomes a Star
Tamar Schlick 259
11. Molecular Dynamics Simulations of RNA Systems:
Importance of the Initial Conditions
Pascal Auffinger 283
12. Molecular Dynamics Simulations of Nucleic Acids
Nad'a Spackovä, Thomas E. Cheatham, III and Jifi Sponer 301
13. Using Computer Simulations to Study Decoding
by the Ribosome
Kevin Y. Sanbonmatsu 327
14. Base Stacking and Base Pairing
Jifi Sponer, Petr Jurecka and Pavel Hobza 343
15. Interaction of Metal Cations with Nucleic Acids
and their Building Units
Judit E. Sponer, Jaroslav V. Burda, Jerzy Leszczynki,
and Jifi Sponer 389
16. Proton Transfer in DNA Base Pairs
J. Bertran, L. Biancafort, M. Noguera, M. Sodupe 411
17. Comparative Study of Quantum Mechanical Methods
Related to Nucleic Acid Bases: Electronic Spectra, Excited
State Structures and Interactions
M.K. Shukla and Jerzy Leszczynski 433
18. Substituent Effects on Hydrogen Bonds in DNA
Celia Fonseca Guerra and F. Matthias Bickelhaupt 463
19. Computational modeling of Charge Transfer in DNA
Alexander A. Voityuk 485
20. Quantum Chemical Calculations of NMR Parameters
Wolfgang Schöfberger, Vladimir Sychrovsky and
Lukas Trantirek 513
Contents vii
21. The Importance of Entropie Factors in DNA Behaviour:
Insights from Simulations
Sarah A. Harris and Charles A. Laughton 537
22. Sequence Dependent Harmonie Deformability of Nucleic
Acids Inferred from Atomistic Molecular Dynamics
Filip Lankas 559
23. Simulation of Equilibrium and Dynamic Properties
of Large DNA Molecules
Alexander Vologodskii 579
24. Chromatin Simulations
J. Langowski and H. Schiessel 605
Index 635 |
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| spelling | Computational studies of RNA and DNA ed. by J. Šponer ... Dordrecht Springer 2006 XI, 636 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Challenges and Advances in Computational Chemistry and Physics 2 Biochemical genetics Computational Biology Computational biology DNA Molecular Biology Molecular dynamics Nucleic Acids Nucleic acids Computer simulation RNA RNS (DE-588)4076759-0 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 gnd rswk-swf Molekulare Bioinformatik (DE-588)4531334-9 s DNS (DE-588)4070512-2 s RNS (DE-588)4076759-0 s DE-604 Šponer, Jiří edt Erscheint auch als Online-Ausgabe 1-4020-4851-3 Challenges and Advances in Computational Chemistry and Physics 2 (DE-604)BV022199777 2 text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2806036&prov=M&dok_var=1&dok_ext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015411712&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computational studies of RNA and DNA Challenges and Advances in Computational Chemistry and Physics Biochemical genetics Computational Biology Computational biology DNA Molecular Biology Molecular dynamics Nucleic Acids Nucleic acids Computer simulation RNA RNS (DE-588)4076759-0 gnd DNS (DE-588)4070512-2 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd |
| subject_GND | (DE-588)4076759-0 (DE-588)4070512-2 (DE-588)4531334-9 |
| title | Computational studies of RNA and DNA |
| title_auth | Computational studies of RNA and DNA |
| title_exact_search | Computational studies of RNA and DNA |
| title_exact_search_txtP | Computational studies of RNA and DNA |
| title_full | Computational studies of RNA and DNA ed. by J. Šponer ... |
| title_fullStr | Computational studies of RNA and DNA ed. by J. Šponer ... |
| title_full_unstemmed | Computational studies of RNA and DNA ed. by J. Šponer ... |
| title_short | Computational studies of RNA and DNA |
| title_sort | computational studies of rna and dna |
| topic | Biochemical genetics Computational Biology Computational biology DNA Molecular Biology Molecular dynamics Nucleic Acids Nucleic acids Computer simulation RNA RNS (DE-588)4076759-0 gnd DNS (DE-588)4070512-2 gnd Molekulare Bioinformatik (DE-588)4531334-9 gnd |
| topic_facet | Biochemical genetics Computational Biology Computational biology DNA Molecular Biology Molecular dynamics Nucleic Acids Nucleic acids Computer simulation RNA RNS DNS Molekulare Bioinformatik |
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