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The Resource Computational studies of RNA and DNA, J. Sponer, F. Lankas (eds.)

Computational studies of RNA and DNA, J. Sponer, F. Lankas (eds.)

Contributor

Language: eng

Work

Publication

Dordrecht, Springer, c2006

Extent: xi, 636 p.

Contents

Machine derived contents note: 1. Basics of Nucleic Acid Structure
Bohdan Schneider and Helen M Berman 1
2. Using Amber to Simulate DNA and RNA
Thomas E. Cheatham, IH and David A. Case 45
3. Theoretical Studies of Nucleic Acids and Nucleic
Acid-Protein Complexes using Charmm
A lexander D. MacKerell, Jr and Lennart Nilsson 73
4. Continuum Solvent Models to Study the Structure
and Dynamics of Nucleic Acids and Complexes with Ligands
Martin Zacharias 95
5 Data Mining of Molecular Dynamic Trajectories
of Nucleic Acids
Modesto Orozco, Agnes Nov, Tim Meyer, Manuel Rueda,
Carles Ferrer, Antonio Valencia, Alberto Pdrez,
Oliver Carrillo, Juan Fernandez-Recio, Xavier de la Cruz
and F. Javier Luque 121
6. Enhanced Sampling Methods for Atomistic Simulation
of Nucleic Acids
Catherine Kelso and Carlos Simmerling 147
7. Modeling DNA Deformation
Peter Varnai and Richard Lavery 169
8. Molecular Dynamics Simulations and Free Energy
Calculations on Protein-Nucleic Acid Complexes
David L. Beveridge, Suijit B. Dixit, Bethany L. Kormos
AInni M' Ban anger and B. Jayaram 211
9. DNA Simulation Benchmarks as Revealed
by X-Ray Structures
fWfnaK. Olson, Andre; V. Colasanti, Eun Li, Wei Ge,
Guohfi Zheng, and ictor B. 7h urkin 235
10. RNA:The Cousin Left Behind Becomes a Star
Tqrpn Sch'ick 250
11. Molecul ar Dynamics Simulations of RNA Systems:
Importance of the Initial Conditions
Pascal Aff/ingei 283
12. Molecular Dynamics Simulations of Nucleic Acids
Sad'a Spackova Thomas E. Checatham, III and Jirl Sponr 301
13. Using Computer Simulations to Study Decoding
by the Ribosome
Kevin Y S anhonatsu 327
14. ase Stacking and Base Paiiing
Ji Sponer cr,Peir Jurecka and Pavel vHota 343
15 Interaction of Metal Cations with Nucleic Acids
and their Building Units
lucit E. Sponer, Jaros/as V. Burda Jrzy Le-szczynki
and Jii Sponer 389
I6. Proton Transfer in DNA Base Pairs
J. Be tan, L Biancafort, M. Noguera, M. Sodupe 411
17 Comparative Study of Quantum Mechanical Methods
Reated to Nucleic Acid Bases: Electronic Spectra, Excited
State Structures and Interactions
U.K. Shukla and Jerzy Leszczynski 433
18. Substituent Effects on Hydrogen Bonds in DNA
Cedlia IFonseca Gueria and F. Matthias Bickelhaupt 463
19. Comput ational modeling of Charge Transfer in DNA
Alexandcr 4. Voit/yk 485
20 Quantum Chemical Calculations of NMR Paameters
Wolfgang Schfber gei , Vladimir Sychrovs/k aind
L ulas Tranti c 513
2. The Importance of Entropic Factors m DNA Behaviour:
Insights from Simulations
Sarah A. Harris and Charles A. Laughton 537
22 Sequence-Dependent Harmonic 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
A Langawski and HL Schiesel 605

Isbn: 9781402047947

Instance

Label: Computational studies of RNA and DNA

Title: Computational studies of RNA and DNA

Statement of responsibility: J. Sponer, F. Lankas (eds.)

Contributor

Subject

Language: eng

Cataloging source: Uk

Dewey number: 572.8

Illustrations: illustrations

Index: index present

LC call number: QP623

LC item number: .C66 2006

Literary form: non fiction

Nature of contents: bibliography

Series statement: Challenges and advances in computational chemistry and physics

Series volume: 2

Label: Computational studies of RNA and DNA, J. Sponer, F. Lankas (eds.)

Publication

Dordrecht, Springer, c2006

Bibliography note: Includes bibliographical references and index

http://library.link/vocab/branchCode

Contents: Machine derived contents note: 1. Basics of Nucleic Acid Structure -- Bohdan Schneider and Helen M Berman 1 -- 2. Using Amber to Simulate DNA and RNA -- Thomas E. Cheatham, IH and David A. Case 45 -- 3. Theoretical Studies of Nucleic Acids and Nucleic -- Acid-Protein Complexes using Charmm -- A lexander D. MacKerell, Jr and Lennart Nilsson 73 -- 4. Continuum Solvent Models to Study the Structure -- and Dynamics of Nucleic Acids and Complexes with Ligands -- Martin Zacharias 95 -- 5 Data Mining of Molecular Dynamic Trajectories -- of Nucleic Acids -- Modesto Orozco, Agnes Nov, Tim Meyer, Manuel Rueda, -- Carles Ferrer, Antonio Valencia, Alberto Pdrez, -- Oliver Carrillo, Juan Fernandez-Recio, Xavier de la Cruz -- and F. Javier Luque 121 -- 6. Enhanced Sampling Methods for Atomistic Simulation -- of Nucleic Acids -- Catherine Kelso and Carlos Simmerling 147 -- 7. Modeling DNA Deformation -- Peter Varnai and Richard Lavery 169 -- 8. Molecular Dynamics Simulations and Free Energy -- Calculations on Protein-Nucleic Acid Complexes -- David L. Beveridge, Suijit B. Dixit, Bethany L. Kormos -- AInni M' Ban anger and B. Jayaram 211 -- 9. DNA Simulation Benchmarks as Revealed -- by X-Ray Structures -- fWfnaK. Olson, Andre; V. Colasanti, Eun Li, Wei Ge, -- Guohfi Zheng, and ictor B. 7h urkin 235 -- 10. RNA:The Cousin Left Behind Becomes a Star -- Tqrpn Sch'ick 250 -- 11. Molecul ar Dynamics Simulations of RNA Systems: -- Importance of the Initial Conditions -- Pascal Aff/ingei 283 -- 12. Molecular Dynamics Simulations of Nucleic Acids -- Sad'a Spackova Thomas E. Checatham, III and Jirl Sponr 301 -- 13. Using Computer Simulations to Study Decoding -- by the Ribosome -- Kevin Y S anhonatsu 327 -- 14. ase Stacking and Base Paiiing -- Ji Sponer cr,Peir Jurecka and Pavel vHota 343 -- 15 Interaction of Metal Cations with Nucleic Acids -- and their Building Units -- lucit E. Sponer, Jaros/as V. Burda Jrzy Le-szczynki -- and Jii Sponer 389 -- I6. Proton Transfer in DNA Base Pairs -- J. Be tan, L Biancafort, M. Noguera, M. Sodupe 411 -- 17 Comparative Study of Quantum Mechanical Methods -- Reated to Nucleic Acid Bases: Electronic Spectra, Excited -- State Structures and Interactions -- U.K. Shukla and Jerzy Leszczynski 433 -- 18. Substituent Effects on Hydrogen Bonds in DNA -- Cedlia IFonseca Gueria and F. Matthias Bickelhaupt 463 -- 19. Comput ational modeling of Charge Transfer in DNA -- Alexandcr 4. Voit/yk 485 -- 20 Quantum Chemical Calculations of NMR Paameters -- Wolfgang Schfber gei , Vladimir Sychrovs/k aind -- L ulas Tranti c 513 -- 2. The Importance of Entropic Factors m DNA Behaviour: -- Insights from Simulations -- Sarah A. Harris and Charles A. Laughton 537 -- 22 Sequence-Dependent Harmonic 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 -- A Langawski and HL Schiesel 605

Control code: 000040987409

Dimensions: 25 cm

Extent: xi, 636 p.

Isbn: 9781402047947

Lccn: 2007398400

Other physical details: ill.

http://library.link/vocab/recordID: .b24048392

System control number

(OCoLC)72867746
springer1402047940

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