Pocket-Finding Algorithms

These 2D and 3D concepts have been implemented into geometry-based pocket finding algorithms (21, 25, 28, 30-41) that are listed in Table 1. 

Energy-based approach The concept of the energy-based pocket finding algorithms is to describe the atomic density at a neighborhood of a probe using potential functions similar to the one used to... 

To conclude this section, we remind that the main purpose of the protein finding algorithms is to localize the cavities within the protein and estimate its size (see Note 4). They do not give information on the druggability of the pocket itself. This is the object of the next section. 

Pocket finder, an online tool, uses energy-based calculations to find the ligandbinding regions. The interface of the server is shown in Fig. 5.13. It follows the LIGSITE algorithm [16]. We can either give the PDB ID or browse the protein of... 

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