Atomic force microscopy (AFM) experiments and steered molecular dynamics (SMD) simulations have revealed much about the dynamics of protein-ligand binding and unbinding, as well as the stretching and unfolding of proteins. Both techniques induce ligand unbinding or protein unfolding by applying exte
Calculating potentials of mean force from steered molecular dynamics simulations
β Scribed by Park, Sanghyun; Schulten, Klaus
- Book ID
- 118748179
- Publisher
- American Institute of Physics
- Year
- 2004
- Tongue
- English
- Weight
- 609 KB
- Volume
- 120
- Category
- Article
- ISSN
- 0021-9606
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Steered molecular dynamics (SMD), a computer simulation method for studying force-induced reactions in biopolymers, has been applied to investigate the response of protein domains to stretching apart of their terminal ends. The simulations mimic atomic force microscopy and optical tweezer experiment
Umbrella samplmg" has been incorporated in the thermodynamic integration method to obtain a potential of mean force by slow growth molecular-dynamics simulations. The method was tested for liquid argon, for which good agreement was obtained with a standard potential of mean force, as derived from th