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Biomolecular Simulations

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Cover of 'Biomolecular Simulations'

Table of Contents

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    Book Overview
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    Chapter 1 Atomistic Force Fields for Proteins
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    Chapter 2 Force Fields for Small Molecules
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    Chapter 3 Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field
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    Chapter 4 Quantum Chemical and QM/MM Models in Biochemistry
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    Chapter 5 A Practical View of the Martini Force Field.
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    Chapter 6 Using SMOG 2 to Simulate Complex Biomolecular Assemblies
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    Chapter 7 Replica-Exchange Methods for Biomolecular Simulations
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    Chapter 8 Metadynamics to Enhance Sampling in Biomolecular Simulations
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    Chapter 9 Protein–Ligand Binding Free Energy Calculations with FEP+
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    Chapter 10 Ligand-Binding Calculations with Metadynamics
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    Chapter 11 The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions
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    Chapter 12 Google-Accelerated Biomolecular Simulations.
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    Chapter 13 A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference
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    Chapter 14 Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods
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    Chapter 15 Modeling Biological Complexes Using Integrative Modeling Platform
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    Chapter 16 Coevolutionary Analysis of Protein Sequences for Molecular Modeling
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    Chapter 17 Coarse Graining of a Giant Molecular System: The Chromatin Fiber
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    Chapter 18 Analyzing Biomolecular Ensembles
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    Chapter 19 Using Data-Reduction Techniques to Analyze Biomolecular Trajectories
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    Chapter 20 Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis
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    Chapter 21 Analyzing and Biasing Simulations with PLUMED
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Title
Biomolecular Simulations
Published by
Springer New York, September 2019
DOI 10.1007/978-1-4939-9608-7
ISBNs
978-1-4939-9607-0, 978-1-4939-9608-7
Editors

Bonomi, Massimiliano, Camilloni, Carlo

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