RE: size of ligand binding pocket

Hello Uwe,
 You may want to take a look at PASS (Putative Active Sites with Spheres).
 Freeware executables are available at:
 http://www.ccl.net/cca/software/UNIX/pass/overview.html
 Hope this helps,
 Pieter
 ----------------
 PASS (Putative Active Sites with Spheres) is a simple computational tool
 that uses geometry to characterize regions of buried volume in proteins and
 to identify positions likely to represent binding sites based upon the size,
 shape, and burial extent of these volumes. PASS'S utility as a predictive
 tool for binding site identification is tested by predicting known binding
 sites of proteins in the PDB using both complexed macromolecules and their
 corresponding apo-protein structures. The results indicate that PASS can
 serve as a front-end to fast docking. The main utility of PASS lies in the
 fact that it can analyze a moderate-size protein (~ 30 kD) in under twenty
 seconds, which makes it suitable for interactive molecular modeling, protein
 database analysis, and aggressive virtual screening efforts. As a modeling
 tool, PASS (i) rapidly identifies favorable regions of the protein surface,
 (ii) simplifies visualization of residues modulating binding in these
 regions, and (iii) provides a means of directly visualizing buried volume,
 which is often inferred indirectly from curvature in a surface
 representation. PASS produces output in the form of standard PDB files,
 which are suitable for any modeling package, and provides script files to
 simplify visualization in Cerius2., InsightII., MOE., Quanta., RasMol., and
 Sybyl.. PASS is freely available to all.
 -----Original Message-----
 From: Uwe Richter [mailto:urichter_at_jerini.de]
 Sent: Wednesday, June 15, 2005 3:50 PM
 To: CCL
 Subject: CCL:size of ligand binding pocket
 Dear CCLers,
 I am looking for software which is able to quantify the
 size/depth of ligand binding pockets of proteins?
 Thanks in advance,
 Uwe
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