From owner-chemistry@ccl.net Sun Jul 19 05:57:01 2009 From: "Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il" To: CCL Subject: CCL:G: center of mass Message-Id: <-39808-090719055434-25726-Go2tmmv4z0ex0XKpXuupvA=-=server.ccl.net> X-Original-From: Tamar Ansbacher Content-Type: multipart/alternative; boundary=00504502d4223a9b9f046f0c0107 Date: Sun, 19 Jul 2009 12:54:17 +0300 MIME-Version: 1.0 Sent to CCL by: Tamar Ansbacher [tamar.ansbacher+/-mail.huji.ac.il] --00504502d4223a9b9f046f0c0107 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Bill any QM package (e.g., gaussian gamess orca etc. ) can give you the standard orientation of the molecule with 0.0 0.0 0.0 at the center of mass Tamar On Sat, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill36=yahoo.co.uk < owner-chemistry:-:ccl.net> wrote: > > Sent to CCL by: "S. Bill" [S_Bill36|a|yahoo.co.uk] > Dear CCL users > I was wonder if you know a simple program can be used to determine and > visualise the center of mass of a molecule. > Thanks in advance > bill> > > --00504502d4223a9b9f046f0c0107 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Bill
any QM package (e.g., gaussian gamess orca etc.= )
can give you the standard orientation of the molecule
with 0.0 0.0= 0.0 at the center of mass
Tamar

On S= at, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill36=3Dyahoo.co.uk <owner-chemistry:-:ccl.net> wrote:

Sent to CCL by: "S. =A0Bill" [S_Bill36|a|yahoo.co.uk]
Dear CCL users
I was wonder if you know a simple program can be used to determine and visu= alise the center of mass of a molecule.
Thanks in advance
bill



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--00504502d4223a9b9f046f0c0107-- From owner-chemistry@ccl.net Sun Jul 19 12:20:01 2009 From: "Subramani K dr.subramanik^^gmail.com" To: CCL Subject: CCL: PDB of CYP2B6 Message-Id: <-39809-090719093302-3073-s1IX5cMDFZm75DtspiowMQ : server.ccl.net> X-Original-From: Subramani K Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 19 Jul 2009 17:48:13 +0530 MIME-Version: 1.0 Sent to CCL by: Subramani K [dr.subramanik%a%gmail.com] Hi all I could not find the PDB files for Cytochrome P450 2B6 at the pdb.org site which has the code as CYP2B6. Can I have P4502C8 instead ( which is available) for docking studies of a drug. Else can someone tell me where I can download this from. Thanks in advance regards Subramani From owner-chemistry@ccl.net Sun Jul 19 14:53:01 2009 From: "Gerard Pujadas gerard.pujadas::gmail.com" To: CCL Subject: CCL: Database of molecules isolated from natural products requiered (with explicit mention to the source/s from which each one is isolated) Message-Id: <-39810-090719143458-18558-0TPh7aCun2NxYKmI5//6Yg*_*server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0016367d6f14cc4125046f12452d Date: Sun, 19 Jul 2009 19:22:57 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas|-|gmail.com] --0016367d6f14cc4125046f12452d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL subscribers, I am looking for free or commercial databases of 2D or 3D molecular structures isolated from natural products (different from the Beilstein database), that mention the source from which each molecule is isolated (and ideally links to the bibliographic reference that describes the method used to isolate each one). I know that ZINC has a natural products subset but the source of the molecules is difficult to find because it is catalog-oriented (and the source is usually not reported in the catalog) ... With many thanks in advances for your help Yours sincerely Best Gerard --0016367d6f14cc4125046f12452d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL subscribers,

I am looking for free or commercial databases = of 2D or 3D molecular structures isolated from natural products (different = > from the Beilstein database), that mention the source from which each molec= ule is isolated (and ideally links to the bibliographic reference that desc= ribes the method used to isolate each one).

I know that ZINC has a natural products subset but the source of the mo= lecules is difficult to find because it is catalog-oriented (and the source= is usually not reported in the catalog) ...

With many thanks in adv= ances for your help

Yours sincerely

Best

Gerard

--0016367d6f14cc4125046f12452d-- From owner-chemistry@ccl.net Sun Jul 19 15:33:00 2009 From: "s. Bill s_bill36[a]yahoo.co.uk" To: CCL Subject: CCL:G: center of mass Message-Id: <-39811-090719084902-32244-PD+CGK0Bwh32DBNRKreSAA^server.ccl.net> X-Original-From: "s. Bill" Content-Type: multipart/alternative; boundary="0-1533796305-1248004126=:67407" Date: Sun, 19 Jul 2009 11:48:46 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: "s. Bill" [s_bill36()yahoo.co.uk] --0-1533796305-1248004126=:67407 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Sorry, but this is a charge center (not mass center). and how can I visualize it. --- On Sun, 19/7/09, Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il wrote: > From: Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il Subject: CCL:G: center of mass To: "Bill, S. H. " Date: Sunday, 19 July, 2009, 9:54 AM Hi Bill any QM package (e.g., gaussian gamess orca etc. ) can give you the standard orientation of the molecule with 0.0 0.0 0.0 at the center of mass=20 Tamar On Sat, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill36=3Dyahoo.co.uk wrote: =0A =0ASent to CCL by: "S. =A0Bill" [S_Bill36|a|yahoo.co.uk] =0ADear CCL users =0AI was wonder if you know a simple program can be used to determine and v= isualise the center of mass of a molecule. =0AThanks in advance =0Abill =0A =0A =0A =0A-=3D This is automatically added to each message by the mailing script = =3D- =0A =0AE-mail to subscribers: CHEMISTRY%ccl.net or use: =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0AE-mail to administrators: CHEMISTRY-REQUEST%ccl.net or use =0A =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message =0A =0A=0A =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml =0A =0A=0A =0A=0A=0A =0A=0A =0A =A0 =A0 =A0http://www.ccl.net/spammers.txt =0A =0A=0A =0A =0A =0A=0A=0A=0A --0-1533796305-1248004126=:67407 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Sorry, but this is a charge center (not mass = center).
and how can I visualize it.


--- On Sun, 19/7/09, = Tamar Ansbacher tamar.ansbacher]*[mail.huji.ac.il <owner-chemistry[]cc= l.net> wrote:

From: Tamar Ansbac= her tamar.ansbacher]*[mail.huji.ac.il <owner-chemistry[]ccl.net>
Su= bject: CCL:G: center of mass
To: "Bill, S. H. " <s_bill36[]yah= oo.co.uk>
Date: Sunday, 19 July, 2009, 9:54 AM

Hi Bill
any QM package (e.g., gaussian gamess= orca etc. )
can give you the standard orientation of the molecule
wi= th 0.0 0.0 0.0 at the center of mass
Tamar

On Sat, Jul 18, 2009 at 10:49 PM, S. Bill S_Bill36=3Dyahoo.co.uk <owner-che= mistry%ccl.net> wrote:
=0A

=0ASent to CCL by: "S.  Bill" [S_Bill36|= a|yahoo.c= o.uk]
=0ADear CCL users
=0AI was wonder if you know a simple prog= ram can be used to determine and visualise the center of mass of a molecule= .
=0AThanks in advance
=0Abill
=0A
=0A
=0A
=0A-=3D This i= s automatically added to each message by the mailing script =3D-
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= =0AE-mail to subscribers: CHEMI= STRY%ccl.net or use:
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<= /blockquote>

=0A=0A=0A=0A --0-1533796305-1248004126=:67407-- From owner-chemistry@ccl.net Sun Jul 19 16:07:00 2009 From: "Elaine Meng meng . cgl.ucsf.edu" To: CCL Subject: CCL: PDB of CYP2B6 Message-Id: <-39812-090719154103-13559-njT3KtWNZeCtjSWrXTHl4Q+/-server.ccl.net> X-Original-From: "Elaine Meng" Date: Sun, 19 Jul 2009 15:41:00 -0400 Sent to CCL by: "Elaine Meng" [meng\a/cgl.ucsf.edu] Hi Subramani, If you enter "p450 2c8" in the search area at http://www.rcsb.org/pdb/ there are at least five structures of the 2C8 isoform (1PQ2 and various complexes of 2C8dH), although all with resolution >2.0 A. I didn't see 2B6 with the same approach, but if that is your primary target you may want to be more creative and try several different variations of the search string, or get the sequence of 2B6 and blast it against the set of PDB sequences. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 19, 2009, at 5:18 AM, Subramani K dr.subramanik^^gmail.com wrote: Sent to CCL by: Subramani K [dr.subramanik%a%gmail.com] Hi all I could not find the PDB files for Cytochrome P450 2B6 at the pdb.org site which has the code as CYP2B6. Can I have P4502C8 instead ( which is available) for docking studies of a drug. Else can someone tell me where I can download this from. Thanks in advance regards Subramani