Understanding the structure and function relationships for proteins and biomolecular assemblies is one of the challenges in the post-genomic era. At the molecular level, molecular dynamics simulations are very powerful but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-receptor binding is the coarse-grained molecular simulations of simplified models, such as the all-atom Go-Model. There have been several methodological advances and novel applications for coarse-grained calculations (i.e., Go models) on biological molecules. Go-models have given promising results for calculating the folding mechanism of real proteins. We propose to use the all-atom Go-model to calculate the binding mechanism of surface proteins to their ligands.
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