How is protein cavity centre related to binding? I am confused and I have the following questions: 1\. What are (in the context of article below) protein cavity centres? 2\. How are they related to binding? (Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study, Santos et a. 2012)

As you can find under the table with cavity centers in pdf version of this article:

> The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are similar to hexoses in shape and/or size. **The cavity center is the centroid of the reported PDB atom numbers.**

And a little later:

> The binding-site center is computed as the hexose pyranose ring centroid for the positive examples, and as the ligand or empty pocket centroid for the negative ones. The hexose pyranose-ring atoms are located up to 2.9 ̊ A away from the ring’s centroid. Since some atomic interactions can be important up to 7 ̊ A [22], we consider the binding-site as all protein atoms present within a 10 ̊ A radius sphere around the binding center. All other atoms are discarded.

So basically @aandreev is right. You can read about centroids here