From chemistry-request@ccl.net Wed May 26 23:26:38 2004 Received: from einstein ([61.11.19.75]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4R4QYAI002214 for ; Wed, 26 May 2004 23:26:36 -0500 Received: (qmail 4307 invoked by uid 0); 27 May 2004 04:31:03 -0000 Received: from unknown (HELO Bohr) (192.168.1.55) by 0 with SMTP; 27 May 2004 04:31:03 -0000 From: "Bhavesh Borate" To: Subject: IC50 to Ki Date: Thu, 27 May 2004 10:08:42 +0530 Message-ID: <000201c443a4$7d095e40$3701a8c0@Bohr> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0003_01C443D2.96C19A40" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 X-Spam-Status: No, hits=3.0 required=7.5 tests=HTML_MESSAGE,NO_RDNS2, WORKSTATION_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0003_01C443D2.96C19A40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Hello All, I have data of lignads in Ki and IC50 values. I need to convert all IC50 values to their corresponding Ki values. Can anyone suggest how to do this ?? Thanks Bhavesh --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.690 / Virus Database: 451 - Release Date: 5/22/2004 ------=_NextPart_000_0003_01C443D2.96C19A40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hello All,

I have data of lignads in = Ki and IC50 values. I need to convert all IC50 = values to their corresponding Ki = values.

Can anyone suggest how to do this = ??

Thanks

Bhavesh

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------=_NextPart_000_0003_01C443D2.96C19A40-- From chemistry-request@ccl.net Thu May 27 08:04:08 2004 Received: from imail-gv5.wyeth.com (imail-gv5.wyeth.com [155.94.60.245]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4RD47hq014937 for ; Thu, 27 May 2004 08:04:07 -0500 Received: from ce08a07m.genetics.com (ce08a07m.ce.us.pri.wyeth.com [10.8.163.107]) by imail-gv5.wyeth.com (Switch-3.0.4/Switch-3.0.0) with ESMTP id i4RD7FTf013968 for ; Thu, 27 May 2004 09:07:15 -0400 (EDT) Received: from USCE03-MTA by ce08a07m.genetics.com with Novell_GroupWise; Thu, 27 May 2004 09:07:15 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Thu, 27 May 2004 09:06:53 -0400 From: "Eric Feyfant" To: , Subject: Re: CCL:IC50 to Ki Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=__Part87A67FFD.0__=" X-Spam-Status: No, hits=2.0 required=7.5 tests=ALUSSINAN_5,HTML_60_70, HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --=__Part87A67FFD.0__= Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi; First you can only estimate a Ki from an IC50, and for that you need to know Substrate concentration, Km and the mode of action (competitive inhibitor, non competitive, un-competitive ....). I suggest you an old paper that I found useful for me: Yung-Chi Cheng and William H Prusoff, Biochemical Pharmacology, Vol22 pp 3099-3108, 1973. Eric >>> "Bhavesh Borate" 5/27/2004 12:38:42 AM >>> Hello All, I have data of lignads in Ki and IC50 values. I need to convert all IC50 values to their corresponding Ki values.Can anyone suggest how to do this ?? Thanks Bhavesh --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.690 / Virus Database: 451 - Release Date: 5/22/2004 --=__Part87A67FFD.0__= Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Description: HTML

Hi;

First you can only estimate a Ki from an IC50, and for that you need to know Substrate concentration, Km and the mode of action (competitive inhibitor, non competitive, un-competitive ....).

I suggest you an old paper that I found useful for me: Yung-Chi Cheng and William H Prusoff, Biochemical Pharmacology, Vol22 pp 3099-3108, 1973.

Eric

>>> "Bhavesh Borate" <bhaveshb/at/VLifeSciences.com> 5/27/2004 12:38:42 AM >>>

Hello All,

I have data of lignads in Ki and IC50 values. I need to convert all IC50 values to their corresponding Ki values.

Can anyone suggest how to do this ??

Thanks

Bhavesh

---
Outgoing mail is certified Virus Free.
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--=__Part87A67FFD.0__=-- From chemistry-request@ccl.net Thu May 27 11:28:36 2004 Received: from mxout6.cac.washington.edu (mxout6.cac.washington.edu [140.142.33.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4RGSZ83029319 for ; Thu, 27 May 2004 11:28:35 -0500 Received: from smtp.washington.edu (smtp.washington.edu [140.142.33.9]) by mxout6.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i4RGVec7026470; Thu, 27 May 2004 09:31:44 -0700 Received: from gonaou (donald.chem.washington.edu [128.95.128.116]) by smtp.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with SMTP id i4RGVeQw010685 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Thu, 27 May 2004 09:31:40 -0700 Message-ID: <001201c44408$163a1970$74805f80@gonaou> From: "Carsten Detering" To: "Bhavesh Borate" , References: <000201c443a4$7d095e40$3701a8c0@Bohr> Subject: Re: CCL:IC50 to Ki Date: Thu, 27 May 2004 18:31:39 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C44418.D99CC3D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=0.1 required=7.5 tests=HTML_70_80,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000F_01C44418.D99CC3D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Bhavesh, have a look at this paper: Cheng et al Biochem Pharmacol. 22, 3099-3108 (1973) Hope this helps, Carsten -------------------------------------------- Carsten Detering =20 University of Washington =20 Department of Chemistry =20 Seattle, WA 98195 =20 Fon 206.543.5081 =20 Fax 206.685.8665 =20 ----- Original Message -----=20 From: Bhavesh Borate=20 To: chemistry=at=ccl.net=20 Sent: Thursday, May 27, 2004 6:38 AM Subject: CCL:IC50 to Ki Hello All, =20 I have data of lignads in Ki and IC50 values. I need to convert all = IC50 values to their corresponding Ki values. Can anyone suggest how to do this ?? =20 Thanks=20 =20 Bhavesh --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.690 / Virus Database: 451 - Release Date: 5/22/2004 ------=_NextPart_000_000F_01C44418.D99CC3D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Bhavesh,

have a look at this paper:

Cheng et al Biochem Pharmacol. 22, = 3099-3108=20 (1973)

Hope this helps,

Carsten

--------------------------------------------
Carsten=20 Detering           = ;      =20
University of Washington
Department of=20 Chemistry
Seattle, WA=20 98195           &n= bsp; =20
Fon=20 206.543.5081          &= nbsp;   =20
Fax=20 206.685.8665          &= nbsp;   =20

----- Original Message -----
From:=20 Bhavesh Borate
To: chemistry=at=ccl.net

Sent: Thursday, May 27, 2004 = 6:38=20 AM

Subject: CCL:IC50 to Ki

Hello=20 All,

I have data of lignads in Ki and = IC50 values. I=20 need to convert all IC50 values to their corresponding Ki values.

Can anyone suggest how = to do this ??

Thanks=20

Bhavesh

---
Outgoing mail is certified Virus = Free.
Checked by=20 AVG anti-virus system (http://www.grisoft.com).
Version: = 6.0.690=20 / Virus Database: 451 - Release Date: 5/22/2004

------=_NextPart_000_000F_01C44418.D99CC3D0-- From chemistry-request@ccl.net Thu May 27 02:38:18 2004 Received: from web15401.mail.cnb.yahoo.com (web15401.mail.cnb.yahoo.com [202.43.216.204]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4R7c2hq017870 for ; Thu, 27 May 2004 02:38:05 -0500 Message-ID: <20040527074107.64071.qmail*at*web15401.mail.cnb.yahoo.com> Received: from [202.196.110.202] by web15401.mail.cnb.yahoo.com via HTTP; Thu, 27 May 2004 15:41:07 CST Date: Thu, 27 May 2004 15:41:07 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: SDF database to Mopac input file To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.6 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,RCVD_IN_RFCI,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I have got a SDF database, I hope to convert it to Mopac input file using BABEL as following: babel -isdf molecule.sdf all -h -omopint molecule.dat -split And then I use the keyword EF supported by Mopac to optimize, however, I find it's very difficult to get a optimized geometry. Is there any other way to do this job? I appreciate you for any suggestions. Regards, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong*at*yahoo.com.cn _________________________________________________________ Do You Yahoo!? OSSJOdL+P!#?QE;"5gSJWTVz@)H]#! http://cn.rd.yahoo.com/mail_cn/tag/10m/*http://cn.mail.yahoo.com/event/10m.html From chemistry-request@ccl.net Thu May 27 02:28:27 2004 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4R7SQhq017347 for ; Thu, 27 May 2004 02:28:26 -0500 Received: from lctn.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA31668; Thu, 27 May 2004 09:32:32 +0200 Sender: moreau-.at.-host20.lctn.uhp-nancy.fr Message-ID: <40B59940.BC455835-.at.-lctn.uhp-nancy.fr> Date: Thu, 27 May 2004 09:31:13 +0200 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: Kadir Diri CC: chemistry-.at.-ccl.net Subject: Re: CCL:freezing atoms in frequency calculations References: <40B1A07E.2000507-.at.-visual1.chem.pitt.edu> Content-Type: multipart/alternative; boundary="------------3BFE143248D664A6AC5D9C22" X-Spam-Status: No, hits=2.0 required=7.5 tests=HTML_20_30,HTML_MESSAGE, LINES_OF_YELLING autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------3BFE143248D664A6AC5D9C22 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Kadir, Gaussian (98 and 03) does that. Just make a frequency job as usual. To freeze a particular atom, put the flag "-1" between the atomic type and the geometrical specifications (for a cartesian input) . If I remember, the "not frozen" atom must not be the first one. Here is an example with methanol (non optimized geometry) : # RHF/STO-3G freq frequency job 0 1 C -1 -1.153515 -.353884 .000000 H -1 -2.064398 .242951 .000000 C -1 .000000 .524697 .000000 H -1 -1.131237 -.982224 .889165 H -1 -1.131237 -.982224 -.889165 O -1 1.171017 -.242584 .000000 H -1 -.022277 1.153036 -.889165 H -1 -.022277 1.153036 .889165 H 1.924381 .331220 .000000 Which lead to 3 frequencies with a negative one. Hope this helps. Yohann Kadir Diri wrote: > Dear all, > I wonder if there is an ab initio code that lets one freeze all atoms > but one in a large molecule, and calculate the frequency related to the > atom which was not not frozen, say, like calculating the frequency of a > single OH stretch in some molecule? > Thank you in advance! > kadir > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY-.at.-ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------3BFE143248D664A6AC5D9C22 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Kadir,

Gaussian (98 and 03) does that. Just make a frequency job as usual. To freeze a particular atom, put the flag "-1"
between the atomic type and the geometrical specifications (for a cartesian input) . If I remember,
the "not frozen" atom must not be the first one.

Here is an example with methanol (non optimized geometry) :

# RHF/STO-3G freq

frequency job

0 1
C   -1   -1.153515 -.353884   .000000
H   -1   -2.064398   .242951   .000000
C   -1     .000000   .524697   .000000
H   -1   -1.131237 -.982224   .889165
H   -1   -1.131237 -.982224 -.889165
O   -1    1.171017 -.242584   .000000
H   -1    -.022277 1.153036 -.889165
H   -1    -.022277 1.153036   .889165
H         1.924381   .331220   .000000

Which lead to 3 frequencies with a negative one.

Hope this helps.

Yohann

Kadir Diri wrote:

Dear all,
I wonder if there is an ab initio code that lets one freeze all atoms
but one in a large molecule, and calculate the frequency related to the
atom which was not not frozen, say, like calculating the frequency of a
single OH stretch in some molecule?
Thank you in advance!
kadir
-= This is automatically added to each message by the mailing script =-
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and send your message to: CHEMISTRY-.at.-ccl.net
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Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page)
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-- 

               Yohann MOREAU, Doctorant                
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html

--------------3BFE143248D664A6AC5D9C22-- From chemistry-request@ccl.net Thu May 27 03:04:48 2004 Received: from web15406.mail.cnb.yahoo.com (web15406.mail.cnb.yahoo.com [202.43.216.209]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4R84Xhq019849 for ; Thu, 27 May 2004 03:04:35 -0500 Message-ID: <20040527080730.28740.qmail~at~web15406.mail.cnb.yahoo.com> Received: from [202.196.110.202] by web15406.mail.cnb.yahoo.com via HTTP; Thu, 27 May 2004 16:07:30 CST Date: Thu, 27 May 2004 16:07:30 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: Why two different results in SYBYL To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.6 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,RCVD_IN_RFCI,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I perform CoMFA using SYBYL 6.7 with CoMFA field obtained by two methods. And I got two different results for the same database. First, I use the default setting, and I got the relative contribution of steric and electrostatic field: 0.310/0.690. And then, I calculated the steric and electrostatic field respectively, and perform PLS analysis on the steric, electrostatic fields and bio-activity data. And got the relative contribution: 0.150/0.850. And the contour maps of CoMFA is also very different. I hope to know why there is such difference. Any suggestions will be really appreciated. Best wishes, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong~at~yahoo.com.cn _________________________________________________________ Do You Yahoo!? OSSJOdL+P!#?QE;"5gSJWTVz@)H]#! http://cn.rd.yahoo.com/mail_cn/tag/10m/*http://cn.mail.yahoo.com/event/10m.html From chemistry-request@ccl.net Thu May 27 04:17:53 2004 Received: from web15410.mail.cnb.yahoo.com (web15410.mail.cnb.yahoo.com [202.43.216.213]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4R9Hbhq026462 for ; Thu, 27 May 2004 04:17:39 -0500 Message-ID: <20040527092044.90952.qmail~at~web15410.mail.cnb.yahoo.com> Received: from [202.196.110.202] by web15410.mail.cnb.yahoo.com via HTTP; Thu, 27 May 2004 17:20:44 CST Date: Thu, 27 May 2004 17:20:44 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: question about "View CoMFA" To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.6 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,RCVD_IN_RFCI,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I wonder why the default settings for "contour specifications" is set to 80% for favored fields, and 20% for unfavored fields. What's the meaning of those settings, for different settings may give different contour maps. How to explain those difference? Any suggestions will be really appreciated! Regards, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong~at~yahoo.com.cn _________________________________________________________ Do You Yahoo!? OSSJOdL+P!#?QE;"5gSJWTVz@)H]#! http://cn.rd.yahoo.com/mail_cn/tag/10m/*http://cn.mail.yahoo.com/event/10m.html From chemistry-request@ccl.net Thu May 27 02:53:55 2004 Received: from nibbel.kulnet.kuleuven.ac.be (nibbel.kulnet.kuleuven.ac.be [134.58.240.41]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4R7rshq019198 for ; Thu, 27 May 2004 02:53:54 -0500 Received: from localhost (localhost [127.0.0.1]) by nibbel.kulnet.kuleuven.ac.be (Postfix) with ESMTP id E88164B58F; Thu, 27 May 2004 09:57:01 +0200 (CEST) Received: from octavianus.kulnet.kuleuven.ac.be (octavianus.kulnet.kuleuven.ac.be [134.58.240.71]) by nibbel.kulnet.kuleuven.ac.be (Postfix) with ESMTP id 19BAA4B463; Thu, 27 May 2004 09:57:01 +0200 (CEST) Received: from rega.kuleuven.ac.be (dommelsch.rega.kuleuven.ac.be [134.58.19.18]) by octavianus.kulnet.kuleuven.ac.be (Postfix) with ESMTP id B57ABAEE34; Thu, 27 May 2004 09:57:00 +0200 (CEST) Sender: mathy{at}ccl.net Message-ID: <40B59FBD.7E32C951{at}rega.kuleuven.ac.be> Date: Thu, 27 May 2004 09:58:53 +0200 From: Matheus Froeyen Organization: REGA Instituut - KU Leuven - Belgium X-Mailer: Mozilla 4.79C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Bhavesh Borate Cc: chemistry{at}ccl.net Subject: Re: CCL:IC50 to Ki References: <000201c443a4$7d095e40$3701a8c0@Bohr> Content-Type: multipart/alternative; boundary="------------0C9FF452B8FD3A27D45F4C82" X-Virus-Scanned: by KULeuven Antivirus Cluster X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_70_80,HTML_MESSAGE, MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------0C9FF452B8FD3A27D45F4C82 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Please take a look at: %A YC Cheng %A WH Prusoff %J Biochemical Pharmacology %D 1973 %V 22 %P 3099-3108 %T Relationship between the inhibition constant (Ki) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Beware that the method is only valid if same conditions are used in the experiments. Regards Mathy ----------------------------------------------- Bhavesh Borate wrote: > Hello All, > > I have data of lignads in Ki and IC50 values. I need to convert all > IC50 values to their corresponding Ki values. > > Can anyone suggest how to do this ?? > > Thanks > > Bhavesh > --- > Outgoing mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.690 / Virus Database: 451 - Release Date: 5/22/2004 --------------0C9FF452B8FD3A27D45F4C82 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,

Please take a look at:

%A YC Cheng %A WH Prusoff
%J Biochemical Pharmacology
%D 1973 %V 22 %P 3099-3108
%T Relationship between the inhibition constant (Ki) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction.

Beware that the method is only valid
if same conditions are used in the experiments.

Regards
Mathy

-----------------------------------------------
Bhavesh Borate wrote:

Hello All,

I have data of lignads in Ki and IC50 values. I need to convert all IC50 values to their corresponding Ki values.
Can anyone suggest how to do this ??

Thanks

Bhavesh
---
Outgoing mail is certified Virus Free.
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--------------0C9FF452B8FD3A27D45F4C82-- From chemistry-request@ccl.net Thu May 27 02:26:35 2004 Received: from mailservice.tudelft.nl (mailservice.tudelft.nl [130.161.131.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4R7QYhq017157 for ; Thu, 27 May 2004 02:26:34 -0500 Received: from localhost (localhost [127.0.0.1]) by rav.antivirus (Postfix) with ESMTP id EF33D32B9 for ; Thu, 27 May 2004 09:29:41 +0200 (MEST) Received: from mail.dct.tudelft.nl (tnw-dct1.dct.tudelft.nl [130.161.196.201]) by mx2.tudelft.nl (Postfix) with ESMTP id 2BF1CED7E for ; Thu, 27 May 2004 09:29:41 +0200 (MEST) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 27 May 04 09:29:42 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 27 May 04 09:29:36 +0200 From: "Karin Gutkowski" Organization: Delft University of Technology (TNW-DCT) To: chemistry{at}ccl.net Date: Thu, 27 May 2004 09:29:32 +0200 MIME-Version: 1.0 Subject: CCL: universal L-J parameters" Message-ID: <40B5B4FB.18277.241F22@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.12a) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body X-Virus-Scanned: by amavisd-new at tudelft.nl X-Spam-Status: No, hits=0.2 required=7.5 tests=BAD_X_HEADERS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I would like to ask you for help for the following issue: I need to use Lenanrd jones molecular parameters (sigma and e/k) in order to adjust my program to the Henry constant, for systems with the following molecules: methane carbon dioxide CO N2 O2 CH3OH C2H5OH I found already some values for the LJ parameters, but they vary a lot depending on the reference. So I would like to have the whole information from only one source. Please, let me know if you can help me with this. Kind regards, Karin Gutkowski emails: K.I.Gutkowski{at}tnw.tudelft.nl gutkowsk{at}cnea.gov.ar From chemistry-request@ccl.net Thu May 27 11:54:06 2004 Received: from med-gwia-01a.med.umich.edu (med-gwia-01a.med.umich.edu [141.214.93.149]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4RGs583030869 for ; Thu, 27 May 2004 11:54:05 -0500 Received: from gwia-01-MTA by med-gwia-01a.med.umich.edu with Novell_GroupWise; Thu, 27 May 2004 12:56:36 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Beta Date: Thu, 27 May 2004 12:56:51 -0400 From: "Renxiao Wang" To: , Subject: Re: CCL:IC50 to Ki Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=1.0 required=7.5 tests=ALUSSINAN_5 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, Bhavesh! I am afraid there is no general solution for this. For some types of binding assays, there are procedures for converting IC50 to Ki values, such as the Cheng-Prusoff equation. Regards, Renxiao -------------------------------------------------------------------------------------------------- Renxiao Wang, Ph.D. Research Investigator Department of Internal Medicine, Hematology/Oncology Division University of Michigan Medical School Ann Arbor, MI 48109, U.S.A. Tel: (734) 764-2449; Fax: (734) 764-2532 E-mail: renxiao_at_med.umich.edu Web: http://sw8.im.med.umich.edu/~arthur/ -------------------------------------------------------------------------------------------------- >>> "Bhavesh Borate" 05/27/04 12:38AM >>> Hello All, I have data of lignads in Ki and IC50 values. I need to convert all IC50 values to their corresponding Ki values. Can anyone suggest how to do this ?? Thanks Bhavesh --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.690 / Virus Database: 451 - Release Date: 5/22/2004 From chemistry-request@ccl.net Thu May 27 07:41:36 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4RCfYhq012537 for ; Thu, 27 May 2004 07:41:35 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HYD00AKII2KPC:at:mailserver.unimi.it> for chemistry:at:ccl.net; Thu, 27 May 2004 14:44:45 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HYD00J1SI2HYP:at:smtp.unimi.it> for chemistry:at:ccl.net; Thu, 27 May 2004 14:44:42 +0200 (MEST) Date: Thu, 27 May 2004 14:49:49 +0200 From: Alessandro Contini Subject: oniom frequency calculation To: chemistry:at:ccl.net Reply-to: alessandro.contini:at:unimi.it Message-id: <200405271449.49613.alessandro.contini:at:unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4RCfahq012545 Dear all, I'm trying to perform some ONIOM calculations on a large system using a two-layer pm3mm:uff level of theory. Optimizations end without problems, however frequency calculations end with the following message: 06734\Na,-27.4589036815,11.3926430179,2.4365411139\\Version=x86-Linux- G03RevB.04\HF=0.7787613\RMSD=0.000e+00\RMSF=5.335e-06\Dipole=-2.518992 4,-0.1589827,-1.5015458\PG=C01 [X(C2147H3284N575Na15O660S25)]\\@ At the touch of love, everyone becomves a poet. -- Plato DoMSJ allocation failure: iend,mxcore= 202419758 33171127 Error termination via Lnk1e in /home/mcae/gaussian03/g03/l9999.exe at Thu May 27 13:44:24 2004. Job cpu time: 0 days 2 hours 38 minutes 12.8 seconds. File lengths (MBytes): RWF= 300 Int= 0 D2E= 0 Chk= 262 Scr= 1 Does anybody has suggestions? Thanks a lot for your help Alessandro -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini:at:unimi.it From chemistry-request@ccl.net Thu May 27 05:26:08 2004 Received: from smbh.smbh.univ-paris13.fr (smbh.smbh.univ-paris13.fr [194.254.171.250]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4RANmhq031940 for ; Thu, 27 May 2004 05:23:58 -0500 Received: from garfield (garfield.smbh.univ-paris13.fr [194.254.171.93]) by smbh.smbh.univ-paris13.fr (8.9.3+Sun/8.9.1) with ESMTP id MAA12096; Thu, 27 May 2004 12:22:22 +0100 (GMT) Subject: Helical parameters extraction from trajectory From: ladam To: chemistry$at$ccl.net, amber$at$scripps.edu Content-Type: text/plain Message-Id: <1085653640.2683.14.camel@garfield> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.4.4-8mdk Date: Thu, 27 May 2004 12:27:21 +0200 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, I would like to extract helical parameters from trajectory files (in trj or dcd format). As far as I know the only way to do it is to extract pdb files from the trajectory and analyse them one by one with the Curves program (R. Lavery). This is rather painfull when dealing with big trajectories, so I'd like to know if someone as a trick or a program to extract helical parameters from trajectories? Thank you -- ------------------------------------------------------------------ | Patrick LADAM | | | Laboratoire CSSB | THE BIG BANG THEORY: | | UFR SMBH | | | 74 rue Marcel Cachin | In the begining there was | | 93017 Bobigny CEDEX | nothing at all. | | >>> NEW e-mail: <<< | | | ladam$at$smbh.smbh.univ-paris13.fr | Then, it exploded... | | Tel: 01 48 38 77 26 / 76 85 | | | Fax: 01 48 38 77 77 | | ------------------------------------------------------------------