Biomolecular Simulations Methods and Protocols

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 Rózycky, 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