From chemistry-request*- at -*ccl.net Thu Jun 16 06:04:59 2005 Received: from mail.nervianoms.com ([217.220.17.130]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GA4vOe001612 for ; Thu, 16 Jun 2005 06:04:57 -0400 Received: from /spool/local by nervianoms.com with [XMail 1.17mod3 (Win32/Ix86) LMAIL Server] for from ; Thu, 16 Jun 2005 10:32:51 +0200 Received: from smtpout1.nervianoms.com (10.206.81.115) by nervianoms.com with [XMail 1.17mod3 (Win32/Ix86) ESMTP Server]; Thu, 16 Jun 2005 10:32:50 +0200 thread-index: AcVyTinx/VcQldKvQ++4WlnoVrS+Vw== Received: from smtpin.nervianoms.com ([10.206.81.115]) by smtpout1.nervianoms.com with Microsoft SMTPSVC(6.0.3790.0); Thu, 16 Jun 2005 10:34:08 +0200 Received: from itnerms020.itner.eu.pnu.com ([10.206.81.108]) by smtpin.nervianoms.com with Microsoft SMTPSVC(6.0.3790.0); Thu, 16 Jun 2005 10:34:08 +0200 Received: by itnerms020.itner.eu.pnu.com with Internet Mail Service (5.5.2653.19) id ; Thu, 16 Jun 2005 10:34:55 +0200 Message-ID: From: "Stouten, Pieter [Nervianoms]" To: Subject: RE: size of ligand binding pocket Date: Thu, 16 Jun 2005 10:34:50 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Class: urn:content-classes:message Importance: normal Priority: normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.3790.0 X-OriginalArrivalTime: 16 Jun 2005 08:34:08.0524 (UTC) FILETIME=[29DC34C0:01C5724E] X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5GA4xOe001618 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 ****************************************************************************** DISCLAIMER AND CONFIDENTIAL NOTICE The information contained in this message and any attachment thereto is to be considered privileged and confidential and is intended for the addressee(s) designated. All rights related to the message itself and its attachments are reserved. If you are not the addressee, any disclosure, reproduction, distribution, on-transmission or use of this communication are strictly prohibited. If you have received this transmission in error, please notify us immediately by return email or telephone and destroy the original message. Le informazioni contenute nel presente messaggio e nei suoi allegati devono essere considerate strettamente confidenziali e riservate esclusivamente ai destinatari indicati. Sono riservati tutti i diritti relativi al messaggio e ai suoi allegati. La lettura, la riproduzione, la diffusione, la ritrasmissione di tutto quanto contenuto nel presente messaggio h consentita esclusivamente ai soggetti destinatari. Se non doveste essere tra i destinatari indicati, ovvero qualora abbiate ricevuto per errore questo messaggio Vi preghiamo di darcene comunicazione e di rimuovere il messaggio stesso e gli allegati dal Vostro sistema.