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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)

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  • $\begingroup$ I don't think this question should be closed. Yet you might want to add a bit more information and references. $\endgroup$
    – cagliari2005
    Commented May 1, 2015 at 4:17
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    $\begingroup$ no need to get hostile. There is a reason number of votes required for closing/putting on hold question. Regarding question: OP, do you have any reference to the phrase used? Isn't "cavity center" is just central point of given cavity? $\endgroup$
    – aaaaa says reinstate Monica
    Commented May 1, 2015 at 5:26

1 Answer 1

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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

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  • $\begingroup$ I could not understand the head or tail of this, can you please tell me if there is any site which clearly explains these calculations?? I am not a biology or chemistry student, I am a computer science student, but my research field is bioinformatics... So i am having a lot of trouble trying to grasp what this thing means.... $\endgroup$
    – girl101
    Commented May 1, 2015 at 13:46
  • $\begingroup$ Could you be more specific, about your problems? $\endgroup$
    – Mithoron
    Commented May 1, 2015 at 14:34
  • $\begingroup$ like where would I find information (calculation and explanations) of obtaining centroids of bonding sites of ligands, I want to know about these binding mechanisms and how these calculations are carried out.. $\endgroup$
    – girl101
    Commented May 1, 2015 at 14:51
  • $\begingroup$ en.wikipedia.org/wiki/Molecular_binding, en.wikipedia.org/wiki/Category:Geometric_centers $\endgroup$
    – Mithoron
    Commented May 3, 2015 at 0:13
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    $\begingroup$ Atomic coordinate are in PDB files of proteins. $\endgroup$
    – Mithoron
    Commented May 5, 2015 at 20:02

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