From owner-chemistry@ccl.net Wed Mar 3 00:39:00 2010 From: "Anthony F kwyjib09[-]gmail.com" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41358-100302155516-736-kyJe7hz6ym7FwcSR9wxRNw||server.ccl.net> X-Original-From: "Anthony F" Date: Tue, 2 Mar 2010 15:55:13 -0500 Sent to CCL by: "Anthony F" [kwyjib09|*|gmail.com] Thanks for everyone previous help on visualizing NBOS. My next question is on visualizing my XYZ files. I have used Avogadro, VMD, and Gabedit. But I want to make diagrams like these: http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif I prefer how the ellipsoids have the 3D effect and that everything is in black and white. I don't like how bonds have two different colors in Avogadro and VMD. Can you guys suggest a program that can visualize those clusters? Thanks Anthony From owner-chemistry@ccl.net Wed Mar 3 09:12:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim-#-compchem.net" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41359-100303035337-501-SvKToa1BbSGTxsA/R4cw1g%%server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=0016e6d7841964e58d0480e19d75 Date: Wed, 3 Mar 2010 08:53:23 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim*o*compchem.net] --0016e6d7841964e58d0480e19d75 Content-Type: text/plain; charset=ISO-8859-1 Dear Anthony This type of visualization is called ORTEP View, generated using ORTEP program. Visit the following link for more information about it and how to download it. http://www.chem.gla.ac.uk/~louis/software/ortep3/ Sincerely; M. Ibrahim On Tue, Mar 2, 2010 at 8:55 PM, Anthony F kwyjib09[-]gmail.com < owner-chemistry[]ccl.net> wrote: > > Sent to CCL by: "Anthony F" [kwyjib09|*|gmail.com] > Thanks for everyone previous help on visualizing NBOS. > > My next question is on visualizing my XYZ files. I have used Avogadro, VMD, > and Gabedit. But I want to make diagrams like these: > > http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif > > I prefer how the ellipsoids have the 3D effect and that everything is in > black and white. I don't like how bonds have two different colors in > Avogadro and VMD. > > Can you guys suggest a program that can visualize those clusters? > > Thanks > > Anthony> > > -- Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim[]compchem.net Website: www.compchem.net Fax No.: +20862342601 --0016e6d7841964e58d0480e19d75 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Anthony
This type of visualization is called ORTEP View, generated= using ORTEP program.
Visit the following link for more informati= on about it and how to download it.=A0
Sinc= erely;
M. Ibrahim

On Tue, Mar 2= , 2010 at 8:55 PM, Anthony F kwyjib09[-]gmail.= com <ow= ner-chemistry[]ccl.net> wrote:

Sent to CCL by: "Anthony =A0F" [kwyjib09|*|gmail.com]
Thanks for everyone previous help on visualizing NBOS.

My next question is on visualizing my XYZ files. I have used Avogadro, VMD,= and Gabedit. But I want to make diagrams like these:

http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif

I prefer how the ellipsoids have the 3D effect and that everything is in bl= ack and white. I don't like how bonds have two different colors in Avog= adro and VMD.

Can you guys suggest a program that can visualize those clusters?

Thanks

Anthony



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=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0Mahmoud A. A. Ibrahim =A0 =A0 =A0 =A0
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 Current Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 7.05, School of Chemistry,
=A0 =A0 =A0 =A0 =A0 =A0 =A0The Universi= ty of Manchester,
=A0 =A0 =A0 =A0 Oxford Road, Manchester, M13 9PL,
=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 United Kingdom.

=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0Home Address
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= Chemistry Department,
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=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Minia Univers= ity,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Minia 61519,
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0Egypt.

= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Contact Information
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--0016e6d7841964e58d0480e19d75-- From owner-chemistry@ccl.net Wed Mar 3 09:47:01 2010 From: "Morad El-Hendawy m80elhendawy-,-yahoo.com" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41360-100303032321-30094-/2fWIdriysETdkT48QFDMw .. server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-1224536481-1267604590=:6794" Date: Wed, 3 Mar 2010 00:23:10 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy . yahoo.com] --0-1224536481-1267604590=:6794 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Yes, ORTEP can do that, it is free. http://www.chem.gla.ac.uk/~louis/software/ortep3/ http://www.ornl.gov/sci/ortep/ortep.html Regards, Morad --- On Tue, 3/2/10, Anthony F kwyjib09[-]gmail.com wrote: > From: Anthony F kwyjib09[-]gmail.com Subject: CCL: Visualizing Software To: "El-Hendawy, Morad Metwally " Date: Tuesday, March 2, 2010, 10:55 PM Sent to CCL by: "Anthony=A0 F" [kwyjib09|*|gmail.com] Thanks for everyone previous help on visualizing NBOS. My next question is on visualizing my XYZ files. I have used Avogadro, VMD,= and Gabedit. But I want to make diagrams like these: http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif I prefer how the ellipsoids have the 3D effect and that everything is in bl= ack and white. I don't like how bonds have two different colors in Avogadro= and VMD. Can you guys suggest a program that can visualize those clusters?=20 Thanks=20 Anthony -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1224536481-1267604590=:6794 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Yes, ORTEP can do that, it is free.
http:/= /www.chem.gla.ac.uk/~louis/software/ortep3/
http://www.ornl.gov/sci/orte= p/ortep.html
Regards,
Morad

--- On Tue, 3/2/10, Anthony F k= wyjib09[-]gmail.com <owner-chemistry[A]ccl.net> wrote:

From: Anthony F kwyjib09[-]gmail.com <owner-c= hemistry[A]ccl.net>
Subject: CCL: Visualizing Software
To: "El-Henda= wy, Morad Metwally " <m80elhendawy[A]yahoo.com>
Date: Tuesda= y, March 2, 2010, 10:55 PM


Sent to CCL = by: "Anthony  F" [kwyjib09|*|gmail.com]
Thanks for everyone previou= s help on visualizing NBOS.

My next question is on visualizing my XY= Z files. I have used Avogadro, VMD, and Gabedit. But I want to make diagram= s like these:

http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ort= ep.gif

I prefer how the ellipsoids have the 3D effect and that e= verything is in black and white. I don't like how bonds have two different = colors in Avogadro and VMD.

Can you guys suggest a program that can = visualize those clusters?

Thanks

Anthony



-= =3D This is automatically added to each message by the mailing script =3D-<= br= l= ook up the X-Original-From: line in the mail header.

E-mail to subsc= ribers: CHEMISTRY[A]ccl.net or use:
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=0A= =0A --0-1224536481-1267604590=:6794-- From owner-chemistry@ccl.net Wed Mar 3 10:23:00 2010 From: "Sergio Emanuel Galembeck segalemb*_*usp.br" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41361-100303080618-25033-dypa6x7Bca3XihurN0f3JA(~)server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 03 Mar 2010 09:06:04 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb(0)usp.br] Dear Anthony, You can try ORTEP3: http://www.chem.gla.ac.uk/~louis/software/ortep3/ Best regards, Sergio Citando "Anthony F kwyjib09[-]gmail.com" : > > Sent to CCL by: "Anthony F" [kwyjib09|*|gmail.com] > Thanks for everyone previous help on visualizing NBOS. > > My next question is on visualizing my XYZ files. I have used > Avogadro, VMD, and Gabedit. But I want to make diagrams like these: > > http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif > > I prefer how the ellipsoids have the 3D effect and that everything > is in black and white. I don't like how bonds have two different > colors in Avogadro and VMD. > > Can you guys suggest a program that can visualize those clusters? > > Thanks > > Anthony> > > From owner-chemistry@ccl.net Wed Mar 3 10:57:00 2010 From: "H.-U. Siehl (Uni ULM) ullrich.siehl!A!uni-ulm.de" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41362-100303024620-25849-h/982r25HND5dlc134li0w^-^server.ccl.net> X-Original-From: "H.-U. Siehl (Uni ULM)" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 03 Mar 2010 08:14:46 +0100 MIME-Version: 1.0 Sent to CCL by: "H.-U. Siehl (Uni ULM)" [ullrich.siehl- -uni-ulm.de] Dear Anthony F. You may want to use: Ortep-3 for Windows: L. J. Farrugia, J. Appl. Cryst (1997), 30, 565. http://www.chem.gla.ac.uk/~louis/software/ortep3/index.html Ortep-3 for Windows is available as a 32-bit executable for all current flavours of Windows (95/98/NT/ME/2000/XP/VISTA). The current release is version 2.02 (released 18th October 2008). It also runs on linux using wine. regards Ulli Anthony F kwyjib09[-]gmail.com wrote: > Sent to CCL by: "Anthony F" [kwyjib09|*|gmail.com] > Thanks for everyone previous help on visualizing NBOS. > > My next question is on visualizing my XYZ files. I have used Avogadro, VMD, and Gabedit. But I want to make diagrams like these: > > http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif > > I prefer how the ellipsoids have the 3D effect and that everything is in black and white. I don't like how bonds have two different colors in Avogadro and VMD. > > Can you guys suggest a program that can visualize those clusters? > > Thanks > > Anthony> > > - From owner-chemistry@ccl.net Wed Mar 3 11:36:01 2010 From: "Jing Kong jkong|,|q-chem.com" To: CCL Subject: CCL: Q-Chem workshop at University of Louisville Message-Id: <-41363-100302180458-20294-fGTBnrz9EEJ11ICOb15S0g]^[server.ccl.net> X-Original-From: "Jing Kong" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0105_01CABA2A.7A15EB10" Date: Tue, 2 Mar 2010 17:04:51 -0500 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong_-_q-chem.com] This is a multi-part message in MIME format. ------=_NextPart_000_0105_01CABA2A.7A15EB10 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear colleague, The Department of Chemistry of the University of Louisville and Q-Chem Inc. would like invite you for one day's workshop entitled: "Advances in methods and applications of electronic structure calculations with Q-Chem program" (http://www.q-chem.com/wslu_hh.html). Q-Chem is a comprehensive ab-initio quantum-chemistry package with capabilities range from the highest performance DFT/HF calculations to high level post-HF correlation methods in electronic structure calculations. Q-Chem tackles a wide range of molecular problems in academic, government and commercial laboratories, including: Molecular Structures Electronic Spectra Chemical Reactions NMR Spectra Molecular Vibrations Solvation Effects Combined QM/MM Method The workshop will take place on March 30th in room W104 of the Ekstrom Library in the University of Louisville, KY at 2301 S. 3rd Street. The workshop will consist of hands-on tutorial sessions, and will provide opportunities to learn basic and advanced features of computational tools in Q-Chem. Please bring your computer laptop for the workshop (Windows 7/Vista/XP preferred). The software can be downloaded from the workshop website (http://www.q-chem.com/wslu_tut.html). There is no charge for attending the workshop, however the space is limited. Please register by March 25th at the registration website (http://www.q-chem.com/wslu_regist.html). We look forward to seeing you at the workshop. I apologize if you have received multiple copies of this announcement. Sincerely, Jing **** Jing Kong, Ph.D., CEO & Chief Scientist, www.q-chem.com ------=_NextPart_000_0105_01CABA2A.7A15EB10 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear colleague,

 =

The Department of Chemistry of the University of Louisville and Q-Chem Inc. = would like invite you for one day's workshop entitled: "Advances in = methods and applications of electronic structure calculations with Q-Chem = program" (http://www.q-chem.com/wslu_hh= .html). 

 =

Q-Chem is a comprehensive ab-initio quantum-chemistry package with capabilities = range > from the highest performance DFT/HF calculations to high level post-HF correlation methods in electronic structure calculations. Q-Chem tackles = a wide range of molecular problems in academic, government and commercial laboratories, including: 

 =

Molecular Structures

Electronic Spectra

Chemical Reactions

NMR Spectra

Molecular Vibrations

Solvation Effects

Combined QM/MM Method 

 =

The workshop will take place on March 30th in room W104 of the Ekstrom = Library in the University of Louisville, KY at 2301 S. 3rd Street. The workshop = will consist of hands-on tutorial sessions, and will provide opportunities to = learn basic and advanced features of computational tools in = Q-Chem. 

 =

Please bring your computer laptop for the workshop (Windows 7/Vista/XP = preferred). The software can be downloaded from the workshop website (http://www.q-chem.com/wslu_t= ut.html). There is no charge for attending the workshop, however the space is = limited. Please register by March 25th at the registration website (http://www.q-chem.com/wsl= u_regist.html). 

 =

We look forward to seeing you at the workshop. 

 =

I apologize if you have received multiple copies of this = announcement.

 =

Sincerely,

 =

Jing

****

Jing Kong, Ph.D., CEO & Chief Scientist, = www.q-chem.com

 

 

------=_NextPart_000_0105_01CABA2A.7A15EB10-- From owner-chemistry@ccl.net Wed Mar 3 12:07:00 2010 From: "Val Gillet v.gillet---sheffield.ac.uk" To: CCL Subject: CCL: Sheffield Chemoinformatics Conference: Registration Open Message-Id: <-41364-100303031045-28542-EEHYao/OGjctcXuO9i3fkQ]^[server.ccl.net> X-Original-From: "Val Gillet" Date: Wed, 3 Mar 2010 03:10:42 -0500 Sent to CCL by: "Val Gillet" [v.gillet,sheffield.ac.uk] Fifth Joint Sheffield Conference on Chemoinformatics University of Sheffield, UK 13th-15th July 2010 http://cisrg.shef.ac.uk/shef2010/ Registration: Registration is now open with early bird discounts available until April 9th. Preliminary Programme: The oral presentations are now listed. Note that there will also be a large number of high quality posters (details to be posted later) following the large response to the call for papers. Commercial exhibition: A list of exhibitors is available. To secure the remaining exhibition slots please email the conference organisers at cheminf2010(a)shef.ac.uk. Organised on behalf of the Molecular Graphics and Modelling Society and the Chemical Structure Association Trust. From owner-chemistry@ccl.net Wed Mar 3 12:41:00 2010 From: "errol lewars elewars]~[trentu.ca" To: CCL Subject: CCL: Stochastic Search for Isomers Message-Id: <-41365-100302172039-25645-6XIs3LqWxGf1ZimdIfkx+w^server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 02 Mar 2010 16:28:01 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars[-]trentu.ca] 2010 March 02 Re stochastic searches for isomers; 1 M. Saunders, "Stochastic search for isomers...", J Comp Chem, 2004, 25(5), 621-626. 2 P P Bera et al., "Mindless Chemistry", J Phys Chem A, 2006, 110(13), 4287-4290. E. Lewars == Dr. Xiaofeng (Frank) Duan duanx.ctr#%#afrl.hpc.mil wrote: > > Sent to CCL by: "Dr. Xiaofeng (Frank) Duan" [duanx.ctr_._afrl.hpc.mil] > Hi all, > > Does anyone know any programs that have features to generate and > filter out stable isomers for a set of atoms (around 8-10 atoms)? > > Thanks! > > Frank Duan > --http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Wed Mar 3 13:43:01 2010 From: "Jamin Krinsky jamink(0)berkeley.edu" To: CCL Subject: CCL: Visualizing Software Message-Id: <-41366-100303130547-24284-9PGASXBTRy3W0blhPcqplA~~server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00163630f673428ba10480e95452 Date: Wed, 3 Mar 2010 10:05:36 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink]![berkeley.edu] --00163630f673428ba10480e95452 Content-Type: text/plain; charset=ISO-8859-1 Dear Anthony, I see you got the needed info about ORTEP, but keep in mind that the graphic you indicated is a drawing from an X-ray diffraction experiment, so the ellipsoids represent thermal motion (and sometimes disorder), which you obviously don't have in a normal computational output. So, your atoms will just come out as banded spheres, in which case you may be better off using VMD and setting everything to grey and black. Regards, Jamin On Tue, Mar 2, 2010 at 12:55 PM, Anthony F kwyjib09[-]gmail.com < owner-chemistry/a\ccl.net> wrote: > > Sent to CCL by: "Anthony F" [kwyjib09|*|gmail.com] > Thanks for everyone previous help on visualizing NBOS. > > My next question is on visualizing my XYZ files. I have used Avogadro, VMD, > and Gabedit. But I want to make diagrams like these: > > http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif > > I prefer how the ellipsoids have the 3D effect and that everything is in > black and white. I don't like how bonds have two different colors in > Avogadro and VMD. > > Can you guys suggest a program that can visualize those clusters? > > Thanks > > Anthony> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink/a\berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --00163630f673428ba10480e95452 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Anthony,
I see you got the needed info about ORTEP, but keep in min= d that the graphic you indicated is a drawing from an X-ray diffraction exp= eriment, so the ellipsoids represent thermal motion (and sometimes disorder= ), which you obviously don't have in a normal computational output. So,= your atoms will just come out as banded spheres, in which case you may be = better off using VMD and setting everything to grey and black.
Regards,
Jamin

On Tue, Mar 2, 2010 at = 12:55 PM, Anthony F kwyjib09[-]gmail.com <owner-chemistry/a\ccl.net> wrote:

Sent to CCL by: "Anthony =A0F" [kwyjib09|*|gmail.com]
Thanks for everyone previous help on visualizing NBOS.

My next question is on visualizing my XYZ files. I have used Avogadro, VMD,= and Gabedit. But I want to make diagrams like these:

http://bhgroup.lsa.umich.edu/files/u1/ge-prop-ortep.gif

I prefer how the ellipsoids have the 3D effect and that everything is in bl= ack and white. I don't like how bonds have two different colors in Avog= adro and VMD.

Can you guys suggest a program that can visualize those clusters?

Thanks

Anthony



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY/a\ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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Before posting, check wait time at: http://www.ccl.net

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Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink/a\berkeley.edu, 510-643-0616
http://glab.cc= hem.berkeley.edu

--00163630f673428ba10480e95452-- From owner-chemistry@ccl.net Wed Mar 3 19:39:00 2010 From: "Veer Shanmugasundaram Veerabahu.Shanmugasundaram.:.pfizer.com" To: CCL Subject: CCL: Call for Abstracts: Using Waters Explicitly in Drug Discovery Message-Id: <-41367-100303193115-6303-lYbOOKSZP67eF+mz2IbF+A:server.ccl.net> X-Original-From: "Veer Shanmugasundaram" Date: Wed, 3 Mar 2010 19:31:11 -0500 Sent to CCL by: "Veer Shanmugasundaram" [Veerabahu.Shanmugasundaram[*]pfizer.com] Water molecules play an integral role in molecular-level biological processes. Substantial enthalpic and entropic energies can be associated with the displacement or bridging of even a single water molecule by a ligand in the binding process. However, the field of computer-aided drug design has largely neglected this important part of the thermodynamic binding process. Typical docking programs and empirical scoring functions either ignore the role of solvent or treat water as a continuous medium. Recent publications suggest that we can use computational methods to estimate in a qualitative and quantitative manner the role of water molecules in binding processes. In this symposium we plan to address the following topics: 1. Thermodynamic characterization of explicit water molecules. For example, quantifying the energy associated with displacing or bridging a water molecule upon binding. 2. Incorporating explicit water molecules into traditional modeling tools. For example, how to include water molecules into the docking process for pose prediction, virtual screening, and rank ordering compounds. 3. Comparative analysis of solvation models for computing binding free energies. For example, when do implicit solvent models succeed and when do they fail due to the finite size, shape, and orientation of explicit water molecules? 4. Analysis and use of water molecules from crystallographic structures. For example, when should we trust the position of a water molecule in a crystal structure? Why do crystal structures of the same target at similar resolutions often have very different numbers and locations of water molecules? Can we use computational tools to improve the process of placing water molecules during the crystal structure refinement process? We are organizing a mini-symposium that will bring together a diverse group of exceptional researchers who have made progress in incorporating waters explicitly in drug discovery. The aim is to highlight state-of-the-art research efforts with an emphasis on practical applications from laboratories in academia and industry. Symposium: Using Waters Explicitly in Drug Discovery Venue: 240th American Chemical Society National Meeting, Boston, MA Dates: August 22-26, 2010 If you would like to submit an abstract to present your work in this mini-symposium, please contact one of us. The deadline for submitting abstracts is March 30th, 2010. Sincerely, Veer & Woody ---- Veer Shanmugasundaram, Ph.D Antibacterials Chemistry/Discovery Technologies, WorldWide Medicinal Chemistry, Pfizer PharmaTherapeutics Research & Development, Eastern Point Road, Groton, CT 06340 Tel:(860)686-9264 Fax:(860)715-3149 Email:Veerabahu.Shanmugasundaram=pfizer.com Woody Sherman, Ph.D Applications Science, Schrodinger Inc New York, NY 10036 Tel:(413)323-0969 Email:Woody.Sherman=schrodinger.com From owner-chemistry@ccl.net Wed Mar 3 21:13:01 2010 From: "Veer Shanmugasundaram Veerabahu.Shanmugasundaram__pfizer.com" To: CCL Subject: CCL: Call for Abstracts: Targeting Gram-Negative Pathogens Symposium Message-Id: <-41368-100303194100-7922-9286R8MfinECTAe7UrbDWQ++server.ccl.net> X-Original-From: "Veer Shanmugasundaram" Date: Wed, 3 Mar 2010 19:40:56 -0500 Sent to CCL by: "Veer Shanmugasundaram" [Veerabahu.Shanmugasundaram---pfizer.com] The emergence of new human bacterial pathogens and increasing antibacterial resistance to existing drugs are critical public health concern especially towards increasingly problematic Gram-negative bacterial pathogens such as Acinetobacter baumannii and Pseudomonas aeruginosa. New classes of antibacterials with novel mechanisms of action and new approaches to increasing the effectiveness of traditional drugs with a quantum leap in our ability to effectively treat these human pathogens is greatly needed. Several such approaches are already being pursued by several laboratories and research organizations across the world. These include characterizing favorable Gram-negative bacterial physico-chemical property space, improving understanding of Gram-negative bacterial cell penetration, improving cell-activity through modulating kinetics and thermodynamics of binding, gaining broad-spectrum against several Gram-negative bacterial strains, strategies to improve resistance profile and selectivity, improving our understanding of efflux pumps and lowering the susceptibility to efflux pumps, using novel influx mechanisms such as siderophore attachments for active transport, targeting novel bacterial mechanisms such as inter-cellular signaling like quorum sensing and early PK and safety considerations in drug development. We plan to organize a mini-symposium that would bring together a diverse group of researchers and scientists who have thought about and applied a variety of drug discovery technologies towards developing anti-bacterial agents targeting Gram-negative pathogens. This session will highlight state-of-the-art research efforts that are ongoing in several laboratories across the world towards the discovery and development of novel AB agents through the use of computational, structural, biophysical and medicinal chemistry based approaches. Symposium: Targeting Gram-Negative Pathogens Venue: 240th American Chemical Society National Meeting, Boston, MA Dates: August 22-26, 2010 If you would like to submit an abstract to present your work in this mini-symposium, please contact one of us. The deadline for submitting abstracts is March 30th, 2010. Sincerely, Veer & Jeremy ---- Veer Shanmugasundaram, Ph.D Antibacterials Chemistry/Discovery Technologies, WorldWide Medicinal Chemistry, Pfizer PharmaTherapeutics Research & Development, Eastern Point Road, Groton, CT 06340 Tel:(860)686-9264 Fax:(860)715-3149 Email:Veerabahu.Shanmugasundaram,+,pfizer.com Jeremy Starr, Ph.D Antibacterials Chemistry/Discovery Technologies, WorldWide Medicinal Chemistry, Pfizer PharmaTherapeutics Research & Development, Eastern Point Road, Groton, CT 06340 Tel:(860)686-1165 Fax:(860)715-3149 Email:Jeremy.Starr,+,pfizer.com