A Practice Tutorial for Predicting Active Site Using SiteMap

2 A Practice Tutorial for Predicting Active Site Using SiteMap 

visuaize and evaluate protein hinting sites 

There is a facility of settings where the user can choose different options as per their requirement. The number of site points for a site (15 default) and the number of sites to be found (5 default) should be specified. Three types of grid are available— fine, standard and coarse—defined based on the distance between two points in the grid. Here, standard grid, the default option, is used. One can also choose between a more restrictive and less restrictive option for defining the hydrophobic regions. Two types of force fields are available of which Optimized Potentials for Liquid Simulations (OPLS) 2005 is the default one. In the given example, all default options are used (Fig. 5.3). 

5 Active Site-Directed Pose Prediction Programs for Efficient... 

Clicking on the start button launches the job, and it takes some time to calculate the score and the results are displayed in the project table (Fig, 5.4). 

---