Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest characteristic measure of a cavity is its volume. The definition of a this volume requires use of a probe. Starting from a set of surface residues accessible to the probe, the cavity volume is defined as a connected volume enclosed by the protein surface and a plane whose intersection with the protein surface defines the outer edge of the enclosing protein surface.

What is a computationally simple (as in ideally "canned", "requiring minimal user input" - a pdb file and probe radius, and perhaps a residue to start searching - and "open-source") way for computation of the volume, probe-accessible surface area, and probe-accessible residues/atoms in such enclosed cavities? Example: assume I want to analyze these basic properties for the volume enclosed by a chaperone such as GroEL. A quick web search turns up a long list of software programs to explore cavities in proteins including CavVis, CavBench, CAVER, and CavityPlus, to name a few, but I am not familiar with many of these, and lack resources for an exhaustive exploration. What would be appropriate software for the task I am interested in?


1 Answer 1


The identification of cavities, for drug design, is beyond the geometric characterization (aka volume).

The server and individual software, beside the geometrical cavity determination, characterize them following their functionality and extent of solvent exposure, what sites are suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors, acceptors, or metal-binding functionality, etc.

Usually, a parameter called druggability is used to score/classify each cavity found.

The reference below can give you a starting point about this type of analysis:

Halgren, T., "Identifying and Characterizing Binding Sites and Assessing Druggability," J. Chem. Inf. Model., 2009, 49, 377–389.

Halgren, T., "New Method for Fast and Accurate Binding-site Identification and Analysis," Chem. Biol. Drug Des., 2007, 69, 146–148.

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    $\begingroup$ Ok, thank you.Seems what you are saying is that the specific software I have listed are not suitable for the task I have in mind because the meaning of cavity in the docking community is not that I have in mind. Then I should modify my question to not refer to specific software. If this drug-binding cavity search software is inappropriate, the question still stands, what would be appropriate software for the task I am interested in? $\endgroup$
    – Buck Thorn
    Commented May 11, 2020 at 18:01
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    $\begingroup$ @BuckThorn I did not get what exactly do you want to do. If you need to identify the cavities and their volume, all software you cite will do. But, if you also want to use them to interact with drugs, then you need to look for the druggability. $\endgroup$
    – Camps
    Commented May 11, 2020 at 18:11
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    $\begingroup$ Ok, thanks for that clarification. It looks like I misread your answer. You were apparently explaining that the software can measure volumes and perform tasks to id druggable targets, but I understood you to say that the software was exclusively for druggability id and would fail to perform the desired volume measurement. Thanks! $\endgroup$
    – Buck Thorn
    Commented May 11, 2020 at 20:55

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