The calculation of free-energy differences by constrained molecular-dynamics simulations
β Scribed by den Otter, W. K.; Briels, W. J.
- Book ID
- 120183516
- Publisher
- American Institute of Physics
- Year
- 1998
- Tongue
- English
- Weight
- 445 KB
- Volume
- 109
- Category
- Article
- ISSN
- 0021-9606
- DOI
- 10.1063/1.477019
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A recently developed method for predicting binding affinities in ligandαreceptor complexes, based on interaction energy averaging and conformational sampling by molecular dynamics simulation, is presented. Polar and nonpolar contributions to the binding free energy are approximated by a linear scali
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In this work, we address two critical aspects of calculation of the free energy differences in molecular systems from molecular simulations. The first aspect involves checking whether the calculated free energy difference depends significantly on the extent of perturbation used for accomplishment of