From owner-chemistry@ccl.net Mon Sep 9 07:24:00 2013 From: "Andrew Voronkov drugdesign[A]yandex.ru" To: CCL Subject: CCL: free software for metabolites prediction Message-Id: <-49154-130909020843-25124-4GyjGPRYmQSs2J3RR2gdPQ[A]server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 09 Sep 2013 10:08:34 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign##yandex.ru] Dear CCL users, are you aware of some free software programs (analogs to MetaCore, MetaSite and MetaDrug for example), which can estimate metabolic transformations and metabolism products for the small molecules? Best regards, Andrew From owner-chemistry@ccl.net Mon Sep 9 07:59:00 2013 From: "Andrew Voronkov drugdesign]|[yandex.ru" To: CCL Subject: CCL: software for toxicity analysis Message-Id: <-49155-130909020955-25182-v3iabS/6xtj6//Kasl0B9Q]|[server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Mon, 09 Sep 2013 10:09:49 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign]~[yandex.ru] Does anyone has any suggestions on this question? Best regards, Andrew -------- ðÅÒÅÓÙÌÁÅÍÏÅ ÓÏÏÂÝÅÎÉÅ -------- 02.09.2013, 23:29, "Andrew Voronkov drugdesign,yandex.ru" : Sent to CCL by: Andrew Voronkov [drugdesign:+:yandex.ru] Dear CCL, I am looking for software, which can be used to analyze the fragments of the substance which cause gastrointestinal toxicity. I have a compound, which displays gastrointestinal toxicity. I would like to analyze groups which may cause it. Please recommend which free online or offline software services can be used for that purpose. Best regards, Andrewššššššhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageššššššhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageššššššhttp://www.ccl.net/chemistry/sub_unsub.shtmlššššššhttp://www.ccl.net/spammers.txt-------- úÁ×ÅÒÛÅÎÉÅ ÐÅÒÅÓÙÌÁÅÍÏÇÏ ÓÏÏÂÝÅÎÉÑ -------- From owner-chemistry@ccl.net Mon Sep 9 11:27:00 2013 From: "Andras Borosy andras.borosy^givaudan.com" To: CCL Subject: CCL: software for toxicity analysis Message-Id: <-49156-130909093232-16895-1TLKhc9hNx1Z/f1QKoDeEw!A!server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 004A6052C1257BE1_=" Date: Mon, 9 Sep 2013 15:32:23 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy**givaudan.com] This is a multipart message in MIME format. --=_alternative 004A6052C1257BE1_= Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 VGhlIE9FQ0QgVG9vbGJveCBtaWdodCBiZSB1c2VmdWw6DQoNCmh0dHA6Ly93d3cub2VjZC5vcmcv 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ZT0yPmh0dHA6Ly93d3cuY2NsLm5ldC9jaGVtaXN0cnkvc2VhcmNoY2NsL2luZGV4LnNodG1sPC9m b250PjwvdHQ+PC9hPjx0dD48Zm9udCBzaXplPTI+PGJyPg0KPGJyPg0KSWYgeW91ciBtYWlsIGJv dW5jZXMgZnJvbSBDQ0wgd2l0aCA1LjcuMSBlcnJvciwgY2hlY2s6PGJyPg0KICZuYnNwOyAmbmJz cDsgJm5ic3A7PC9mb250PjwvdHQ+PGEgaHJlZj1odHRwOi8vd3d3LmNjbC5uZXQvc3BhbW1lcnMu dHh0Pjx0dD48Zm9udCBzaXplPTI+aHR0cDovL3d3dy5jY2wubmV0L3NwYW1tZXJzLnR4dDwvZm9u dD48L3R0PjwvYT48dHQ+PGZvbnQgc2l6ZT0yPjxicj4NCjxicj4NClJURkk6IDwvZm9udD48L3R0 PjxhIGhyZWY9aHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlv bnMvPjx0dD48Zm9udCBzaXplPTI+aHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNj bC9pbnN0cnVjdGlvbnMvPC9mb250PjwvdHQ+PC9hPjx0dD48Zm9udCBzaXplPTI+PGJyPg0KPGJy Pg0KPGJyPg0KPC9mb250PjwvdHQ+DQo8YnI+DQo= --=_alternative 004A6052C1257BE1_=-- From owner-chemistry@ccl.net Mon Sep 9 12:02:00 2013 From: "Patrik Rydberg pry**sund.ku.dk" To: CCL Subject: CCL: free software for metabolites prediction Message-Id: <-49157-130909101354-18597-+1JNJ+GJr8niOPfHyMaiCw~!~server.ccl.net> X-Original-From: Patrik Rydberg Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 9 Sep 2013 14:12:19 +0000 MIME-Version: 1.0 Sent to CCL by: Patrik Rydberg [pry(a)sund.ku.dk] If you are looking for P450 mediated metabolism there are two that are easily accessible and working that can suggest the site of metabolism (without giving you the actual product) SMARTCyp http://www.farma.ku.dk/smartcyp/ (download and web server) RS-Predictor http://reccr.chem.rpi.edu/Software/RS-WebPredictor/ (only available online) There is also an implementation of SMARTCyp in the ToxTree software which actually gives you the product structure http://toxtree.sourceforge.net/ (download) And for general metabolism (enzyme non-specific) there is MetaPrint2D, which predict sites of metabolism, and has an experimental implementation of metabolite prediction as well http://www-metaprint2d.ch.cam.ac.uk/metaprint2d/ MetaPrint2D is also implemented in Bioclipse http://www.bioclipse.net/ There are some other ones as well, but I'm not that familiar with how updated and easily accessible they are, or exactly what they can do OECD QSAR Toolbox http://www.oecd.org/env/ehs/risk-assessment/theoecdqsartoolbox.htm SOMEViz http://www.ncbi.nlm.nih.gov/pubmed/22894162 MetaPred http://crdd.osdd.net/raghava/metapred/ Best regards, Patrik Rydberg -----Original Message----- > From: owner-chemistry+pry==sund.ku.dk!A!ccl.net [mailto:owner-chemistry+pry==sund.ku.dk!A!ccl.net] On Behalf Of Andrew Voronkov drugdesign[A]yandex.ru Sent: Monday, September 09, 2013 08:09 To: Patrik Rydberg Subject: CCL: free software for metabolites prediction Sent to CCL by: Andrew Voronkov [drugdesign##yandex.ru] Dear CCL users, are you aware of some free software programs (analogs to MetaCore, MetaSite and MetaDrug for example), which can estimate metabolic transformations and metabolism products for the small molecules? Best regards, Andrewhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Sep 9 13:19:00 2013 From: "Jed Zaretzki zaretj*_*gmail.com" To: CCL Subject: CCL: free software for metabolites prediction Message-Id: <-49158-130909114613-14451-bQVNL7jnqiiDfdA/hUKhvg_-_server.ccl.net> X-Original-From: Jed Zaretzki Content-Type: multipart/alternative; boundary=001a1133eaca3cfa1004e5f5491e Date: Mon, 9 Sep 2013 10:46:05 -0500 MIME-Version: 1.0 Sent to CCL by: Jed Zaretzki [zaretj|a|gmail.com] --001a1133eaca3cfa1004e5f5491e Content-Type: text/plain; charset=ISO-8859-1 There are two free webservers for predicting CYP-mediated metabolism on drug-like molecules. RS-Predictor - http://reccr.chem.rpi.edu/Software/RS-WebPredictor/ and SMARTCyp - http://www.farma.ku.dk/smartcyp/ Cheers, Jed Zaretzki On Mon, Sep 9, 2013 at 1:08 AM, Andrew Voronkov drugdesign[A]yandex.ru < owner-chemistry===ccl.net> wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign##yandex.ru] > Dear CCL users, are you aware of some free software programs (analogs to > MetaCore, MetaSite and MetaDrug for example), which can estimate metabolic > transformations and metabolism products for the small molecules? > > Best regards, > Andrew> > > -- Jed Zaretzki, Ph.D. Postdoctoral Research Associate Department of Pathology and Immunology Washington University School of Medicine --001a1133eaca3cfa1004e5f5491e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
There are two free webservers for predicting CYP-mediated = metabolism on drug-like molecules.

Cheers,
Jed Zaretzki


On Mon, Sep 9, 2013 at 1:08 AM, Andrew Voronkov drugdesign[A]yandex.ru <owner-chemistry===ccl.net>= wrote:

Sent to CCL by: Andrew Voronkov [drugdesign##yandex.ru]
Dear CCL users, are you aware of some free software programs (analogs to Me= taCore, MetaSite and MetaDrug for example), which can estimate metabolic tr= ansformations and metabolism products for the small molecules?

Best regards,
Andrew



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--
Jed Zaretzki= , Ph.D.
Postdoctoral Research Associate
Department of Pathology and I= mmunology
Washington University School of Medicine --001a1133eaca3cfa1004e5f5491e--