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Biomolecular Simulations, 1st ed. 2019 Methods and Protocols Methods in Molecular Biology Series, Vol. 2022

Langue : Anglais

Coordonnateurs : Bonomi Massimiliano, Camilloni Carlo

Couverture de l’ouvrage Biomolecular Simulations
This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
 
Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.

Foreword…
Preface…
Table of Contents…
Contributing Authors…

PART I ATOMISTIC AND COARSE-GRAINED FORCE FIELDS FOR PROTEINS, SMALL MOLECULES, AND NUCLEIC ACIDS

1. Atomistic Force Fields for Proteins
Robert B. Best

2. Force Fields for Small Molecules
Fang-Yu Lin and Alexander D. MacKerell, Jr.

3. Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field
Ilyas Yildirim

4. Quantum Chemical and QM/MM Models in Biochemistry
Patricia Saura, Michael Röpke, Ana P. Gamiz-Hernandez, and Ville R. I. Kaila

5. A Practical View of the Martini Force Field
Bart M. H. Bruininks, Paulo C. T. Souza, and Siewert J. Marrink

6. Using SMOG 2 to Simulate Complex Biomolecular Assemblies
Mariana Levi, Prasad Bandarkar, Huan Yang, Ailun Wang, Udayan Mohanty, Jeffrey K. Noel, and Paul C. Whitford 

PART II ENHANCED SAMPLING AND FREE-ENERGY CALCULATIONS

7. Replica Exchange Methods for Biomolecular Simulations
Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, and Suyong Re

8. Metadynamics to Enhance Sampling in Biomolecular Simulations
Jim Pfaendtner

9. Protein-Ligand Binding Free Energy Calculations with FEP+
Lingle Wang, Jennifer Chambers, and Robert Abel

10. Ligand Binging Calculations with Metadynamics
Davide Provasi

11. The Adaptive Path Collective Variable - A Versatile Biasing Approach to compute the Average Transition Path and Free Energy of Molecular Transitions
Alberto Pérez de Alba Ortíz, Jocelyne Vreede, and Bernd Ensing 

12. Google-Accelerated Biomolecular Simulations
Kai J. Kohlhoff

PART III INTEGRATIVE APPROACHES FOR BIOMOLECULAR SIMULATIONS

13. A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics using Metainference
Thomas Löhr, Carlo Camilloni, Massimiliano Bonomi, and Michele Vendruscolo

14. Inferring Structural Ensembles of Flexible and Dynamic Macromolecules using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods
Jürgen Köfinger, Bartosz Różycky, and Gerhard Hummer

15. Modeling Biological Complexes using Integrative Modeling Platform
Daniel Saltzberg, Charles H. Greenberg, Shruthi Viswanath, Ilan Chemmama, Ben Webb, Riccardo Pellarin, Ignacia Echeverria, and Andrej Sali

16. Co-Evolutionary Analysis of Protein Sequences for Molecular Modeling
Duccio Malinverni and Alessandro Barducci 

17. Coarse Graining of a Giant Molecular System: The Chromatin Fiber
Guido Tiana and Luca Giorgietti
 
PART IV ANALYZING, VISUALIZING, AND COMPARING BIOMOLECULAR SIMULATIONS
18. Analyzing Biomolecular Ensembles
Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth, Juan Salamanca Viloria, Emmanuelle Bignon, and Elena Papaleo

19. Using Data-Reduction Techniques to Analyze Biomolecular Trajectories
Gareth A. Tribello and Piero Gasparotto

20. Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis
Toni Giorgino

21. Analyzing and Biasing Simulations with PLUMED
Giovanni Bussi and Gareth A. Tribello

Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts

Date de parution :

Ouvrage de 600 p.

17.8x25.4 cm

Disponible chez l'éditeur (délai d'approvisionnement : 15 jours).

Prix indicatif 232,09 €

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