http://www.sas.com/apps/demosdow= nloads/jmptrial8_PROD__sysdep.jsp?packageID=3D000503&jmpflag=3DY

=A0

2009/11/3 amit dong dongamit123]=3D[gmail.com <owner-chemistry[*]ccl.net>

Hi,

=A0

I want to analyse the distribution of my inhibitors and non-inhibitors= using PCA. Is there any tool that can be used for the same? I have already= calculated the descriptors for both the groups.

=A0

Thanks

AD

--000feaf081203fa1a5047788c249-- From owner-chemistry@ccl.net Wed Nov 4 10:17:01 2009 From: "steinbrt[]rci.rutgers.edu" To: CCL Subject: CCL: Request Message-Id: <-40606-091104093315-30654-kC3jADUAzy4UQ8MwUVg/HA(-)server.ccl.net> X-Original-From: steinbrt%x%rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 4 Nov 2009 08:32:06 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: steinbrt=rci.rutgers.edu Hi Basma, in my experience, sulfate ions in an X-ray structure often come from the crystalisation buffer and may be considered crystalisation artifacts, i.e., those ions would not be there in the 'true' solution structure of the protein. The pockets they occupy may simply be water filled, contain a different ion or may undergo conformational changes. If your docking method contains a detailed description of electrostatics, then the ions may influence your results. If they are far away from the binding site, their influence will probably be minor though. Kind Regards, Thomas On Wed, November 4, 2009 6:55 am, Basma Ghazal basmaghazal%x%ymail.com wrote: > Hi, > There are 2� sulfate ion on my pdb structure . > I wonder if this ions separate with crystalization if so, > what about the pocket they occupied? > Does it effect on my docking results? > Thanks, Dr. Thomas Steinbrecher BioMaps Institute Rutgers University 610 Taylor Rd. Piscataway, NJ 08854 From owner-chemistry@ccl.net Wed Nov 4 11:57:01 2009 From: "Werner K werner.schroedinger-x-googlemail.com" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40607-091104115245-13017-XnKohn8YlVvx9BI8GNcv6g]~[server.ccl.net> X-Original-From: "Werner K" Date: Wed, 4 Nov 2009 11:52:41 -0500 Sent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com] Hi, what are in your opinion the best softwares, free and commercial, for protein homology modeling and loop refinement? Thanks WS From owner-chemistry@ccl.net Wed Nov 4 13:59:00 2009 From: "Marcin Krol mykrol]|[cyf-kr.edu.pl" To: CCL Subject: CCL: Homology modeling and loop refinement Message-Id: <-40608-091104134702-16070-81+17j4dScK9Hg7UX0c+Ew\a/server.ccl.net> X-Original-From: Marcin Krol Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Wed, 04 Nov 2009 19:11:25 +0100 MIME-Version: 1.0 Sent to CCL by: Marcin Krol [mykrol(-)cyf-kr.edu.pl] Hi Try the POPULUS server (and a standalone version), it performed quite well in the recent CASP http://www.bmm.icnet.uk/~populus/ Best marcin > Sent to CCL by: "Werner K" [werner.schroedinger^-^googlemail.com] > Hi, > > what are in your opinion the best softwares, free and commercial, for protein homology modeling and loop refinement? > > Thanks > > WS> > -- Dr Marcin Krol Zaklad Bioinformatyki i Telemedycyny Collegium Medicum Uniwersytet Jagiellonski e-mail: mykrol_+_cyf-kr.edu.pl From owner-chemistry@ccl.net Wed Nov 4 20:45:00 2009 From: "Zhong jie liang zjliang:-:mail.shcnc.ac.cn" To: CCL Subject: CCL:G: L401 problem Message-Id: <-40609-091104204318-13332-dJ8a2gwrjCrNKZf9eB1NGQ|server.ccl.net> X-Original-From: "Zhong jie liang" Date: Wed, 4 Nov 2009 20:43:14 -0500 Sent to CCL by: "Zhong jie liang" [zjliang__mail.shcnc.ac.cn] Dear experts: When I did ONIOM caculation. There was error message as follows: Harris functional with IExCor= 402 diagonalized for initial guess. ExpMin= 1.61D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=1 IRadAn= 1 AccDes= 1.00D-06 HarFok: IExCor= 402 AccDes= 1.00D-06 IRadAn= 1 IDoV=1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 Spurious integrated density or basis function: NE= 159 NElCor= 0 El error=7.68D-02 rel=4.83D-04 Tolerance=1.00D-03 Shell 49 absolute error=3.65D-02 Tolerance=1.20D-02 Shell 77 signed error=1.89D-04 Tolerance=1.00D-01 Inaccurate quadrature in CalDSu. Error termination via Lnk1e in /home_soft/home/simm14/program/g03/l401.exe Can anyone give some suggestion? Thanks! Zhongjie Liang zjliang,+,mail.shcnc.ac.cn From owner-chemistry@ccl.net Wed Nov 4 22:09:00 2009 From: "ros rodrigogalindo^^gmail.com" To: CCL Subject: CCL: PCA analysis tool Message-Id: <-40610-091104112455-8568-+GhX4eaWQ3iMthEwCRFPIQ%%server.ccl.net> X-Original-From: ros Content-Type: multipart/alternative; boundary=0016e646432cf4ea5a04778d04f7 Date: Wed, 4 Nov 2009 09:11:04 -0600 MIME-Version: 1.0 Sent to CCL by: ros [rodrigogalindo:-:gmail.com] --0016e646432cf4ea5a04778d04f7 Content-Type: text/plain; charset=ISO-8859-1 2009/11/3 Rajarshi Guha rajarshi.guha[#]gmail.com > > Sent to CCL by: Rajarshi Guha [rajarshi.guha_+_gmail.com] > > On Nov 3, 2009, at 5:46 PM, amit dong dongamit123]=[gmail.com wrote: > > Hi, >> >> I want to analyse the distribution of my inhibitors and non-inhibitors >> using PCA. Is there any tool that can be used for the same? I have already >> calculated the descriptors for both the groups. >> > > Hello! > You can use SIMCA-P from umetrics. http://www.umetrics.com/default.asp/pagename/software_simcapplus/c/3 Its not free but has a working demo so you can try it. I've used it before and recommend it. Cheers! Rodrigo. > > ---------------------------------------------------- > Rajarshi Guha | NIH Chemical Genomics Center > http://www.rguha.net | http://ncgc.nih.gov > ---------------------------------------------------- > Gravity brings me down.http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016e646432cf4ea5a04778d04f7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

2009/11/3 Rajarshi Guha rajarshi.guha[#]= gmail.com <owner-chemistry : ccl.net>
=

Sent to CCL by: Rajarshi Guha [rajarshi.guha_+_gmail.com]

On Nov 3, 2009, at 5:46 PM, amit dong dongamit123]=3D[gmail.com wrote:

Hi,

I want to analyse the distribution of my inhibitors and non-inhibitors usin= g PCA. Is there any tool that can be used for the same? I have already calc= ulated the descriptors for both the groups.

Hello!

You can use SIMCA-P from umetrics.
h= ttp://www.umetrics.com/default.asp/pagename/software_simcapplus/c/3

Its not free but has a working demo so you can try it.=A0 I've used= it before and recommend it.

Cheers!
Rodrigo.

----------------------------------------------------
Rajarshi Guha =A0 =A0 =A0 =A0| NIH Chemical Genomics Center
http://www.rguha.net= | http://ncgc.nih.gov
----------------------------------------------------
Gravity brings me down.

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