From chemistry-request@ccl.net Thu Apr 8 14:04:55 2004 Received: from neptune.tranzymepharma.com (neptune.med.usherbrooke.ca [132.210.158.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i38J4sjR029969 for ; Thu, 8 Apr 2004 14:04:55 -0500 Received: from mercure.neokimia.com (exchange.tranzymepharma.com [192.168.1.3]) by neptune.tranzymepharma.com (8.12.10/8.12.10) with ESMTP id i38J51Qg015130 for ; Thu, 8 Apr 2004 15:05:01 -0400 Content-Class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C41D9C.623C463C" Subject: FW: calculate accessible surface area for an occluded cavity X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Thu, 8 Apr 2004 15:04:57 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: calculate accessible surface area for an occluded cavity thread-index: AcQdMh00qKO+dTeHTw2qV9K32Yp29QAaJ5iAAABocoA= From: "Axel Mathieu" To: "CCL" X-NK-Spam-Status: Ce message n'est pas du SPAM, (Score: 2.787, Requis: 5, FVGT_u_HAS_2LETTERFLDR,HTML_70_80,HTML_MESSAGE,J_CHICKENPOX_39,OACYS_SINGLE,RM_rb_ANCHOR,RM_rb_BREAK,RM_rb_DIV,RM_rb_FONT) X-NK-Spam-Version: SpamAssassin version 2.63 X-Scanned-By: MIMEDefang 2.42 This is a multi-part message in MIME format. ------_=_NextPart_001_01C41D9C.623C463C Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Qin, =20 Take a look at the freeware STC (Structure-based thermodynamic = calculations - these are based on SAS) developped by the PENCE/CIHR = group in Canada http://www.pence.ca/software/stc/html-4.3/stc.html. I = used STC to propose a cholesterol transfer mechanism for the StAR = protein (it conatins a cavity!). In case you're interested, my you'll = find my paper abstract and reference at: = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve = = &db=3Dpubmed&dopt=3DAbstract&list_uids=3D12459035 =20 STC can quickly report the SAS for each heavy atom of a residue and you = just have to add them up, or fill the cavity with the ligand and = calculate the difference (supposing your ligand fills the cavity) ... =20 APM =20 =20 -----Original Message----- From: Q [mailto:qzou.-at-.iupui.edu]=20 Sent: 7 avril, 2004 20:30 To: chemistry.-at-.ccl.net Subject: CCL:calculate accessible surface area for an occluded cavity =20 Dear All, I have a protein with an internal cavity that has no access to the = outside solvent. I would like to calculate the accessible surface area = of the residues inside the cavity to see how accessible they are to the = cavity. How can I do this or what programs could help to do it? How = about NACCESS? Thanks for any input. =20 Qin =20 ------_=_NextPart_001_01C41D9C.623C463C Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Qin,

 

Take a look at the freeware STC (Structure-based thermodynamic calculations = -=A0 these are based on SAS) developped = by the PENCE/CIHR group in Canada http://www.pe= nce.ca/software/stc/html-4.3/stc.html. I used STC to propose a cholesterol transfer mechanism for the StAR = protein (it conatins a cavity!). In case you’re interested, my you’ll = find my paper abstract and reference at: http://www.ncbi= .nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubmed&dopt=3D= Abstract&list_uids=3D12459035

 

STC can quickly report the SAS for each heavy atom of a residue and you just = have to add them up, or fill the cavity with the ligand and calculate the = difference (supposing your ligand fills the cavity) = …

 

APM

 

 

-----Original = Message-----
From: Q = [mailto:qzou.-at-.iupui.edu]
Sent: 7 avril, 2004 20:30
To: chemistry.-at-.ccl.net
Subject: = CCL:calculate = accessible surface area for an occluded cavity

 

Dear = All,

 I have a protein with = an internal cavity that has no access to the outside solvent. I would like = to calculate the accessible surface area of the residues inside the cavity = to see how accessible they are to the cavity. How can I do this or what = programs could help to do it? How about NACCESS? Thanks for any = input.

 

Qin

 

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