PTE (Poceket Tunnel Extraction) package includes basically two schemes of extracting pockets and tunnels from PDB. One is based on the stable manifold of critical points and the other is based on evolution of level set function.

X. Zhang, C. Bajaj
Extraction, Visualization and Quantification of Protein Pockets
Proc. of the 6th Annual International Conference on Computational Systems Bioinformatics, CSB2007, vol 6, pp. 275 - 286, http://tinyurl.com/PMID17951831PMID, : 17951831

• These two packages have been wrapped in TexMol.

These two schemes have been documented in TexMol user guide.