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Home > Biomolecular Simulations: Methods and Protocols > Metadynamics to Enhance Sampling in Biomolecular Simulations
Biomolecular Simulations: Methods and Protocols |
Massimiliano Bonomi; Carlo Camilloni
Springer New York
Biomolecular Simulations: Methods and Protocols
Metadynamics to Enhance Sampling in Biomolecular Simulations
Authors

Jim Pfaendtner

ARI Id

1665206931039_5362493

Access

Not Available Free

Pages

179-200

DOI

10.1007/978-1-4939-9608-7_8

Chapter URL

https://rd.springer.com/protocol/10.1007/978-1-4939-9608-7_8

Table of Contents of Book
Showing 1 to 20 of 27 entries
Chapters/HeadingsAuthor(s)PagesInfo
Front Matter
i-xiii
Front Matter
1-1
Atomistic Force Fields for Proteins
Robert B. Best
3-19
Force Fields for Small Molecules
Fang-Yu Lin; Alexander D. MacKerell Jr
21-54
Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field
Ilyas Yildirim
55-74
Quantum Chemical and QM/MM Models in Biochemistry
Patricia Saura; Michael Röpke; Ana P. Gamiz-Hernandez; Ville R. I. Kaila
75-104
A Practical View of the Martini Force Field
Bart M. H. Bruininks; Paulo C. T. Souza; Siewert J. Marrink
105-127
Using SMOG 2 to Simulate Complex Biomolecular Assemblies
Mariana Levi; Prasad Bandarkar; Huan Yang; Ailun Wang; Udayan Mohanty; Jeffrey K. Noel et al.
129-151
Front Matter
153-153
Replica-Exchange Methods for Biomolecular Simulations
Yuji Sugita; Motoshi Kamiya; Hiraku Oshima; Suyong Re
155-177
Metadynamics to Enhance Sampling in Biomolecular Simulations
Jim Pfaendtner
179-200
Protein–Ligand Binding Free Energy Calculations with FEP+
Lingle Wang; Jennifer Chambers; Robert Abel
201-232
Ligand-Binding Calculations with Metadynamics
Davide Provasi
233-253
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; Bernd Ensing
255-290
Google-Accelerated Biomolecular Simulations
Kai J. Kohlhoff
291-309
Front Matter
311-311
A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference
Thomas Löhr; Carlo Camilloni; Massimiliano Bonomi; Michele Vendruscolo
313-340
Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods
Jürgen Köfinger; Bartosz Różycki; Gerhard Hummer
341-352
Modeling Biological Complexes Using Integrative Modeling Platform
Daniel Saltzberg; Charles H. Greenberg; Shruthi Viswanath; Ilan Chemmama; Ben Webb; Riccardo Pellarin et al.
353-377
Coevolutionary Analysis of Protein Sequences for Molecular Modeling
Duccio Malinverni; Alessandro Barducci
379-397
Chapters/HeadingsAuthor(s)PagesInfo
Showing 1 to 20 of 27 entries
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