Advances in Free-Energy Calculations Based on Classical Molecular Dynamics Simulations
Niels Hansen
- 01 Jan 2014
3
About: The article was published on 01 Jan 2014. and is currently open access. The article focuses on the topics: Molecular dynamics.
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Citations
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Efficient use of non-equilibrium measurement to estimate free energy differences for molecular systems
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References
Free energy of hydrophobic hydration: A molecular dynamics study of noble gases in water
TL;DR: In this paper, the potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied, and the free energy of hydration of the inert gases serves as a simple but illustrative example.
Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.
TL;DR: Important classes of compounds that performed suboptimally with OPLS_2005 show significant improvements and the results with popular small molecule force fields-OPLS_2005, GAFF, and CHARMm-MSI are compared.
294
A Comparison of Methods to Compute the Potential of Mean Force
TL;DR: In this paper, the authors compared different methods to compute PMF for a pair of methane molecules in aqueous solution, and analyzed all combinations of the type of sampling (unbiased, umbrella-biased or constraint-biased), how to compute free energies (from density of states or force averaging) and the type (internal or Cartesian) used for the PMF degree of freedom.
284
A minimal sequence code for switching protein structure and function
TL;DR: It is shown that an IgG-binding, 4β+α fold can be transformed into an albumin- binding, 3-α fold via a mutational pathway in which neither function nor native structure is completely lost.
281
Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
Julien Michel,Jonathan W. Essex +1 more
TL;DR: The purpose of this article is to provide an overview of the current capabilities of free energy calculations and to discuss the applicability of this technology to drug discovery.
277