Tools To Identify Binding Pockets By Geometry

Question

[Burlappsack]

Hello, I am interested in determining concave regions of a protein with the assumption that these are possible binding sites. Has anyone had any success using these determinations, if so, what program did you find useful? So far I have found Ligsite, Surfnet, PocketFinder, & qSiteFinder, but would like to expand my list of possible tools, ideally where the source code is freely available. Thank you very much for your time. Adam.

[Khader Shameer]

It will be nice if you can add URLs to your questions.

Answer 1

[Khader Shameer]

You may add PocketDepth from PocketSuite to your list.

Manuscript is here.

Answer 2

[Woa]

http://compbio.cs.princeton.edu/concavity/

http://strcomp.protein.osaka-u.ac.jp/ghecom/

Source codes are available for both

Try to get a recent review article