Subject: RE: size of ligand binding pocket

From: "Stouten, Pieter [Nervianoms]" <Pieter.Stouten_at_nervianoms.com>
Date: Thu, 16 Jun 2005 10:34:50 +0200

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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