| Description |
1 online resource (xiii, 581 pages) : illustrations (some color) |
| Series |
Methods in molecular biology, 1940-6029 ; volume 2022 |
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Methods in molecular biology (Clifton, N.J.) ; v. 2022. 1064-3745
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| Contents |
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 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 Röpke, 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 Pérez de Alba Ortíz, 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 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 MethodsJürgen Köfinger, Bartosz Różycky, 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 |
| Bibliography |
Includes bibliographical references and index |
| Notes |
Online resource; title from PDF title page (SpringerLink, viewed August 28, 2019) |
| Subject |
Biomolecules -- Simulation methods -- Laboratory manuals
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Molecular biology -- Simulation methods -- Laboratory manuals
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Molecular Biology
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Molecular Dynamics Simulation
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Computer Simulation
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Models, Molecular
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simulation.
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| Genre/Form |
Laboratory manuals
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Laboratory manuals.
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Manuels de laboratoire.
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| Form |
Electronic book
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| Author |
Bonomi, Massimiliano, editor
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Camilloni, Carlo, editor
|
| ISBN |
9781493996087 |
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1493996088 |
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149399607X |
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9781493996070 |
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