## Abstract The standard (absolute) binding free energy of the antibiotic sparsomycin with the 50S bacteria ribosomal subunit is calculated using molecular dynamics (MD) free energy perturbation (FEP) simulations with restraining potentials developed by Wang __et al.__ [Biophys. J. 91:2798โ2814 (20
Free Energy Calculations of Sparsomycin Analogs Binding to the Ribosome with Molecular Dynamics Simulations
โ Scribed by Ge, Xiaoxia; Roux, Benoit
- Book ID
- 119204871
- Publisher
- Biophysical Society
- Year
- 2009
- Tongue
- English
- Weight
- 37 KB
- Volume
- 96
- Category
- Article
- ISSN
- 0006-3495
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๐ SIMILAR VOLUMES
A recently developed method for predicting binding affinities in ligandแreceptor 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
## Abstract The constants of binding of five peptide analogs to the active site of the HIVโ1 asparticโprotease are calculated based on a novel sampling scheme that is efficient and does not introduce any approximations in addition to the energy function used to describe the system. The results agre