Biomolecular Simulations. Methods and Protocols

PART I ATOMISTIC AND COARSE-GRAINED FORCE FIELDS FOR PROTEINS, SMALL MOLECULES, AND NUCLEIC ACIDS
1. Atomistic Force Fields for ProteinsRobert B. Best
2. Force Fields for Small MoleculesFang-Yu Lin and Alexander D. MacKerell, Jr.
3. Improvement of RNA Simulations with Torsional Revisions of the AMBER Force FieldIlyas Yildirim
4. Quantum Chemical and QM/MM Models in BiochemistryPatricia Saura, Michael Roepke, Ana P. Gamiz-Hernandez, and Ville R. I. Kaila
5. A Practical View of the Martini Force FieldBart M. H. Bruininks, Paulo C. T. Souza, and Siewert J. Marrink
6. Using SMOG 2 to Simulate Complex Biomolecular AssembliesMariana 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 SimulationsYuji Sugita, Motoshi Kamiya, Hiraku Oshima, and Suyong Re
8. Metadynamics to Enhance Sampling in Biomolecular SimulationsJim Pfaendtner
9. Protein-Ligand Binding Free Energy Calculations with FEP+Lingle Wang, Jennifer Chambers, and Robert Abel
10. Ligand Binging Calculations with MetadynamicsDavide Provasi
11. The Adaptive Path Collective Variable - A Versatile Biasing Approach to compute the Average Transition Path and Free Energy of Molecular TransitionsAlberto Perez de Alba Ortiz, Jocelyne Vreede, and Bernd Ensing
12. Google-Accelerated Biomolecular SimulationsKai J. Kohlhoff

PART III INTEGRATIVE APPROACHES FOR BIOMOLECULAR SIMULATIONS
13. A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics using MetainferenceThomas Loehr, Carlo Camilloni, Massimiliano Bonomi, and Michele Vendruscolo
14. Inferring Structural Ensembles of Flexible and Dynamic Macromolecules using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement MethodsJurgen Koefinger, Bartosz Rozycky, and Gerhard Hummer
15. Modeling Biological Complexes using Integrative Modeling PlatformDaniel 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 ModelingDuccio Malinverni and Alessandro Barducci
17. Coarse Graining of a Giant Molecular System: The Chromatin FiberGuido Tiana and Luca Giorgietti PART IV ANALYZING, VISUALIZING, AND COMPARING BIOMOLECULAR SIMULATIONS 18. Analyzing Biomolecular EnsemblesMatteo 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 TrajectoriesGareth A. Tribello and Piero Gasparotto
20. Analysis Libraries for Molecular Trajectories: A Cross-Language SynopsisToni Giorgino
21. Analyzing and Biasing Simulations with PLUMEDGiovanni Bussi and Gareth A. Tribello

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.