Verfügbarkeit: Computational studies of RNA and DNA

Computational studies of RNA and DNA:

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Bibliographische Detailangaben
Weitere Verfasser:	Šponer, Jiří (HerausgeberIn)
Format:	Buch
Sprache:	English
Veröffentlicht:	Dordrecht Springer 2006
Schriftenreihe:	Challenges and Advances in Computational Chemistry and Physics 2
Schlagworte:	Biochemical genetics Computational Biology Computational biology DNA Molecular Biology Molecular dynamics Nucleic Acids Nucleic acids > Computer simulation RNA RNS DNS Molekulare Bioinformatik
Online-Zugang:	Inhaltstext Inhaltsverzeichnis
Beschreibung:	XI, 636 S. Ill., graph. Darst.
ISBN:	1402047940 9781402047947

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Datensatz im Suchindex

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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
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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
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