From owner-chemistry@ccl.net Wed Jan 2 02:40:01 2008 From: "Shaillay Dogra shaillay-*-strandls.com" To: CCL Subject: CCL: Modeling Challenge Results Message-Id: <-35957-080102023741-31397-MT6U0O+Iomwm1tCkS/6kqg===server.ccl.net> X-Original-From: Shaillay Dogra Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 2 Jan 2008 13:04:28 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Shaillay Dogra [shaillay::strandls.com] Hi All, The results of the QSARWorld Modeling Challenge 2007 have been declared. http://www.qsarworld.com/qsar-challenge-results.php A collated report on the modeling efforts of the final submissions can be accessed here: http://www.qsarworld.com/files/QSAR_Modeling_Challenge_2007_Submissions.pdf Regards, Shaillay Dogra Scientific-Editor (QSAR-World) http://www.qsarworld.com/ From owner-chemistry@ccl.net Wed Jan 2 08:09:00 2008 From: "David E Clark david.clark]~[argentadiscovery.com" To: CCL Subject: CCL: Virtual screening success stories Message-Id: <-35958-080102072830-8243-D7zuo+GS+2jQeIZKLozYSQ]~[server.ccl.net> X-Original-From: "David E Clark" Date: Wed, 2 Jan 2008 07:28:25 -0500 Sent to CCL by: "David E Clark" [david.clark^^^argentadiscovery.com] Hi all I'd be very interested in learning of any cases where virtual screening has demonstrably (i.e., proven via publication or conference presentation)led to compounds either on the market or that have entered the clinic. Many thanks David From owner-chemistry@ccl.net Wed Jan 2 08:44:01 2008 From: "sina T reli sinatureli-*-gmail.com" To: CCL Subject: CCL: Solvent Accessibility Calcultion (not prediction..) Server Message-Id: <-35959-080102080957-11251-VthzCcAUNqu6Iv+2AZKPLQ:_:server.ccl.net> X-Original-From: "sina T reli" Date: Wed, 2 Jan 2008 08:09:54 -0500 Sent to CCL by: "sina T reli" [sinatureli() gmail.com] Hello, I am interested in webservers that will calculate and rate the solven accessibility of protein residues, given their 3d structure in the format of a pdb file. I have found many servers where they try to predict the solvent accessibility given the sequence. I am NOT interested in that, what I want is very accurate solvent accessibility of proteins whose tertiary structures are known. And also I know that many programs can generate this surface but I need a webserver which will output accessibility as comparable values. I had found this, but the server isnt working for about 4 days. http://pauli.utmb.edu/cgi-bin/get_a.cgi thanks in advance for your kind help From owner-chemistry@ccl.net Wed Jan 2 09:24:01 2008 From: "Carsten Detering detering!=!biosolveit.de" To: CCL Subject: CCL: Virtual screening success stories Message-Id: <-35960-080102092006-18308-mQgbazzxsHxkiqSAsLLzkw]![server.ccl.net> X-Original-From: "Carsten Detering" Date: Wed, 2 Jan 2008 09:20:02 -0500 Sent to CCL by: "Carsten Detering" [detering.:.biosolveit.de] Hi Dave, Happy New Year to you (and of course, all other CClers... ;-) ) Check out this paper from Hugo Kubinyi: Success Stories of Computer-Aided Design in Computer Applications in Pharmaceutical Research and Development, Wiley 2006 Cheers, Carsten __________________________________________________________________ Dr. Carsten Detering; Appl. Scientist detering]-[biosolveit.de Phone: +49-2241-2525-0 / Fax: -525 www.biosolveit.de BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261 >Hi all > >I'd be very interested in learning of any cases where virtual screening has >demonstrably (i.e., proven via publication or conference presentation)led to >compounds either on the market or that have entered the clinic. > >Many thanks >David From owner-chemistry@ccl.net Wed Jan 2 10:02:01 2008 From: "Tiejun Cheng tjcheng[*]mail.sioc.ac.cn" To: CCL Subject: CCL: on comparision of similarity of protein-ligand intera Message-Id: <-35961-080102095650-10687-JuTdBQlAwEamcQk8duHl8A()server.ccl.net> X-Original-From: "Tiejun Cheng" Date: Wed, 2 Jan 2008 09:56:46 -0500 Sent to CCL by: "Tiejun Cheng" [tjcheng(-)mail.sioc.ac.cn] Dear CCLers Any suggested papers on comparision (or description) of similarity of protein-ligand interaction? Thanks in advance and wish you all a happy new year. JAY From owner-chemistry@ccl.net Wed Jan 2 10:35:01 2008 From: "Dominic Ryan dominic.ryan/./comcast.net" To: CCL Subject: CCL: Virtual screening success stories Message-Id: <-35962-080102101612-26002-GVIAUuinoCohbJ/+hSItHA]|[server.ccl.net> X-Original-From: Dominic Ryan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 02 Jan 2008 09:46:10 -0500 MIME-Version: 1.0 Sent to CCL by: Dominic Ryan [dominic.ryan###comcast.net] Hello David, While that would be interesting, I don't think that metric makes a useful comment about the value of virtual screening in pharmaceutical discovery, perhaps you have a different aim in mind. The equation troubles me because it raises false expectations when that link is found. The purpose of virtual screening is to find viable chemical starting points, not proto-drugs. Would you suggest that virtual screening is able to find chemical matter that has an intrinsic high probability of leading to successful PK/PD and tox properties? How would you the application of in silico measures to other sources of chemical matter not from virtual screening? Would you discount the 'success' of virtual screening if some of that success come from methods applied across the board? If a compound class is dropped in LO was it a failure of the screening method, no matter what the method? It is very difficult to make a fair assessment of the value of virtual screening for those reasons -you don't get to run the control experiment, but if we think of it as a tool we can look for places where that tool has value. I would love to hear about virtual screening efforts that were able to identify chemical matter with different properties from other approaches, where none was found by traditional methods, or where virtual screening was able to satisfy a time line not practical for other methods at the time in a project. Dominic Ryan DRI David E Clark david.clark]~[argentadiscovery.com wrote: > Sent to CCL by: "David E Clark" [david.clark^^^argentadiscovery.com] > Hi all > > I'd be very interested in learning of any cases where virtual screening has demonstrably (i.e., proven via publication or conference presentation)led to compounds either on the market or that have entered the clinic. > > Many thanks > David> > > > From owner-chemistry@ccl.net Wed Jan 2 12:59:01 2008 From: "xiaojf a mail.shcnc.ac.cn fdu.xiaojf a gmail.com" To: CCL Subject: CCL: How to fix part of the ligand in docking? Message-Id: <-35963-080102100658-19143-JulwBGzs4E1ASkLE0T+sNw[*]server.ccl.net> X-Original-From: "xiaojf|mail.shcnc.ac.cn" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 02 Jan 2008 22:31:37 +0800 MIME-Version: 1.0 Sent to CCL by: "xiaojf||mail.shcnc.ac.cn" [fdu.xiaojf||gmail.com] Hi all, I'm trying to investigate the interactions between a fatty acid chain (which is attached to holo-ACP) and a protein. We have determined the X-ray structure of the complex of the protein and holo-ACP, but the fatty acid chain cannot be determined by X-ray. So I want to get the final conformation of the fatty acid chain in the binding pocket by docking. And my question is how to fix ACP with its phosphopantetheine chain and let the fatty acid chain move during docking ? Is it feasible, or maybe there are some other better ways? Thanks a lot. From owner-chemistry@ccl.net Wed Jan 2 13:34:00 2008 From: "Elaine C Meng meng(!)cgl.ucsf.edu" To: CCL Subject: CCL: Solvent Accessibility Calculations Message-Id: <-35964-080102122611-18350-Nd3vAJyGrNJwwhi7h6egzA*_*server.ccl.net> X-Original-From: "Elaine C Meng" Date: Wed, 2 Jan 2008 12:26:08 -0500 Sent to CCL by: "Elaine C Meng" [meng*cgl.ucsf.edu] Hello, For GetArea, try this URL instead: http://pauli.utmb.edu/cgi-bin/get_a_form.tcl GetArea is the only server I know of that gives accessibility as a percentage of the "unfolded" accessibility for each amino acid residue. However, there are other servers that will calculate the raw surface area values, for example: http://helixweb.nih.gov/structbio/basic.html the "Calculate" options include MSMS molecular surface and molecular surface (Gerstein). You can get the results graphically or as text listing the surface area of each atom. Elaine ----- Elaine C. Meng, Ph.D. meng###cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Wed Jan 2 14:28:00 2008 From: "Mire Zloh mire.zloh .. ntlworld.com" To: CCL Subject: CCL: Solvent Accessibility Calcultion (not prediction..) Server Message-Id: <-35965-080102104531-13647-y+gCr+eSyyz9uA+o1zoVZA*server.ccl.net> X-Original-From: "Mire Zloh" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 2 Jan 2008 15:14:16 -0000 MIME-Version: 1.0 Sent to CCL by: "Mire Zloh" [mire.zloh.:.ntlworld.com] Hi, MolMol software will give you output of SASA values for the each residue of the PDB file (the surface can also be deconvoluted for each atom as well). http://hugin.ethz.ch/wuthrich/software/molmol/ The values are comparable. In case of NMR ensemle of structures, you would also get range of SASA for each residue. Hope this helps. Mire An example output is enclosed. 1 ARG+ 152.1, 40.8% of 372.6 2 PRO 51.3, 19.6% of 262.2 ... 55 CYS 7.0, 2.8% of 255.1 56 GLY 30.3, 14.9% of 203.8 57 GLY 57.6, 29.3% of 196.6 58 ALA 166.4, 72.4% of 229.8 Total surface: 4084.7 1 ARG+ 155.4 (115.5..198.7), 42.1% ( 30.8.. 54.7) of 369.0 (346.6..380.9) 2 PRO 44.4 ( 24.6.. 57.5), 17.0% ( 9.4.. 22.2) of 260.8 (257.6..264.0) .... 55 CYS 5.8 ( 0.3.. 14.9), 2.3% ( 0.1.. 5.9) of 255.3 (248.7..261.6) 56 GLY 35.9 ( 10.1.. 66.4), 17.7% ( 5.0.. 32.3) of 202.4 (196.1..207.8) 57 GLY 51.9 ( 12.7.. 80.8), 26.0% ( 6.4.. 40.2) of 199.3 (195.9..202.9) 58 ALA 132.7 ( 31.9..173.4), 57.9% ( 14.0.. 77.3) of 229.2 (222.4..234.0) Total surface: 4136.5 ( 3986.5.. 4321.6) -----Original Message----- > From: owner-chemistry ~ ccl.net [mailto:owner-chemistry ~ ccl.net] Sent: 02 January 2008 13:10 To: Zloh, Mire Subject: CCL: Solvent Accessibility Calcultion (not prediction..) Server Sent to CCL by: "sina T reli" [sinatureli() gmail.com] Hello, I am interested in webservers that will calculate and rate the solven accessibility of protein residues, given their 3d structure in the format of a pdb file. I have found many servers where they try to predict the solvent accessibility given the sequence. I am NOT interested in that, what I want is very accurate solvent accessibility of proteins whose tertiary structures are known. And also I know that many programs can generate this surface but I need a webserver which will output accessibility as comparable values. I had found this, but the server isnt working for about 4 days. http://pauli.utmb.edu/cgi-bin/get_a.cgi thanks in advance for your kind helphttp://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 Wed Jan 2 15:03:00 2008 From: "Feng Cheng need47{}gmail.com" To: CCL Subject: CCL: on comparison of similarity of protein ligand interaction Message-Id: <-35966-080102095419-8548-n+Ozm/18DBLnSHt+qIhqcg _ server.ccl.net> X-Original-From: "Feng Cheng" Date: Wed, 2 Jan 2008 09:54:15 -0500 Sent to CCL by: "Feng Cheng" [need47#gmail.com] Dear CCLers Any suggested papers on comparision (or description) of similarity of protein-ligand interaction? Thanks in advance and wish you all a happy new year. JAY From owner-chemistry@ccl.net Wed Jan 2 17:11:01 2008 From: "Duy Le ttduyle|-|gmail.com" To: CCL Subject: CCL: Transition Dipole Moment between excited states with DALTON 2.0 Message-Id: <-35967-080102170836-16992-5GFurxzs5vQRM84ZKtpeZA . server.ccl.net> X-Original-From: "Duy Le" Date: Wed, 2 Jan 2008 17:08:31 -0500 Sent to CCL by: "Duy Le" [ttduyle{=}gmail.com] Hi CCLers, I do want to calculate the Transition Dipole Moment between excited states with DALTON 2.0 at DFT level. However, the output ends by: <<<<<<<<<< OUTPUT FROM RESPONSE INPUT PROCESSING >>>>>>>>>> That's all, I did not get any further result from this point. Any help is appreciated. Happy new year. Here is the input file: -------------------------------- **DALTON INPUT .RUN RESPONSE **INTEGRALS .DIPLEN **WAVE FUNCTION .DFT B3LYP **RESPONSE *QUADRATIC .DIPLEN .DOUBLE RESIDUE .ROOTS 5 0 0 0 **END OF DALTON INPUT ------------------------------ From owner-chemistry@ccl.net Wed Jan 2 17:45:01 2008 From: "Diego Vicente Moreno Rodriguez dvmorenor*|*unal.edu.co" To: CCL Subject: CCL:G: what program can calculate the electrical properties of polymers Message-Id: <-35968-080102171025-17117-adt7VlczUyYyJAHbkK4vKw=-=server.ccl.net> X-Original-From: "Diego Vicente Moreno Rodriguez" Content-Type: multipart/alternative; boundary="----=_Part_4456_18991990.1199311801037" Date: Wed, 2 Jan 2008 17:10:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Diego Vicente Moreno Rodriguez" [dvmorenor^^unal.edu.co] ------=_Part_4456_18991990.1199311801037 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Wei WANG before going any further on your own, i suggest you have a look at the WanT package ( http://www.wannier-transport.org/ ) cheers Diego Moreno 2007/12/30, Praveen Kumar Shrivastava praveenshrivastav]-[gmail.com < owner-chemistry]~[ccl.net>: > > Dear Wei WANG > It is not possible for Gaussian 03 proogram to calculate all these > properties. > with my best wihses and happy new year > praveen > On Dec 20, 2007 12:50 AM, Wei WANG wangwei(0)ciac.jl.cn < > owner-chemistry^^ccl.net > wrote: > > > > > Sent to CCL by: "Wei WANG" [wangwei[a]ciac.jl.cn] > > > > Dear CCLers, > > > > Could you please advice me what program can calculate the electrical > > properties of polymers, especially the high polymers? The electrical > > properties of polymers refers to the behavior and the various physical > > phenomena of polymers under the externally applied electric field, such= as > > polarizations, dielectric constants, dielectric losses, dielectric > > breakdowns, dielectric strengths, electrostatic phenomena, conductiviti= es. > > We have been doing experiments mainly on the high polymers films, and a= t > > present we are trying to do some calculations. Could you please tell me= what > > program can calculate one or some of the electrical properties of polym= ers? > > Whether the Gaussian 03 program can calculate the polymers' electrical > > properties or not? > > > > Best regards, > > > > Wei WANG > > > > > > > > E-mail to subscribers: CHEMISTRY^^ccl.net or > > use: > > > > > > E-mail to administrators: > > > > CHEMISTRY-REQUEST^^ccl.net or use> > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > > > > > --=20 ---- ___ ___ ___ /\ \ /\ \ /\ \ /::\ \ /::\ \ \:\ \ Diego Moreno /:/\:\__\\:\:\__\ /::\__\ \:\:\/__/ \::/ //:/\/__/ Grupo de Qu=EDmica Te=F3rica \::/ / /:/ / \/__/ Universidad Nacional de Col. \/__/ \/__/ ------=_Part_4456_18991990.1199311801037 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear Wei WANG


before going any further on your own, i suggest yo= u have
a look at the WanT package ( http://www.wannier-transport.org/ )

cheers

Diego Moreno

2007/12/30, Praveen Kumar Shrivastava praveenshrivastav]-[gmail.com < owner-chemistry]~[ccl.net>:
Dear Wei WANG
It is not possible for  Gaussian 03 proogram to calculate all the= se properties.
with my best wihses and happy new year
praveen
On Dec 20, 2007 12:50 AM, Wei WANG wangwei(0)cia= c.jl.cn <owner-chemistry= ^^ccl.net > wrote:

Sent to CCL b= y: "Wei  WANG" [wangwei[a]ciac.jl.cn]

Dear CCLers,
Could you please advice me what program can calculate the electrical proper= ties of polymers, especially the high polymers? The electrical properties o= f polymers refers to the behavior and the various physical phenomena of pol= ymers under the externally applied electric field, such as polarizations, d= ielectric constants, dielectric losses, dielectric breakdowns, dielectric s= trengths, electrostatic phenomena, conductivities. We have been doing exper= iments mainly on the high polymers films, and at present we are trying to d= o some calculations. Could you please tell me what program can calculate on= e or some of the electrical properties of polymers? Whether the Gaussian 03= program can calculate the polymers' electrical properties or not?

Best regards,

Wei WANG



E-mail to subscribers:= CHEMISTRY^^ccl.net or use:      

E-mail to administrators: CHEMISTRY-REQUEST^^ccl.net or use
     

Subscribe/Unsubscribe= :
     

Before posting, che= ck wait time at:=20 http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

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--
----   &= nbsp;           &nbs= p;          ___ &nbs= p;   ___     ___  
  &= nbsp;           &nbs= p;            &= nbsp; /\  \   /\  \   /\  = ;\  
         &nb= sp;            =       /::\  \ /::\  \&nbs= p; \:\  \
Diego Moreno      = ;         /:/\:\__\\:\:\__\ /::\__\
            = ;            &n= bsp;  \:\:\/__/ \::/  //:/\/__/
Grupo de Qu=EDmica Te=F3r= ica    \::/  /  /:/  / \/= __/  
Universidad Nacional de Col. \/__/   \/__/ ------=_Part_4456_18991990.1199311801037-- From owner-chemistry@ccl.net Wed Jan 2 20:30:01 2008 From: "Ivanciuc, Ovidiu I. oiivanci~!~utmb.edu" To: CCL Subject: CCL: Solvent Accessibility Calcultion: Getarea is working fine Message-Id: <-35969-080102193850-30210-bdq0JDAV4heSV8GMhZU1Bw|a|server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 2 Jan 2008 18:38:18 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci=-=utmb.edu] >>I had found this, but the server isnt working for about 4 days. >>http://pauli.utmb.edu/cgi-bin/get_a.cgi I just checked GETAREA, http://pauli.utmb.edu/cgi-bin/get_a_form.tcl and it works fine. If you still have problems running this program, you may contact me directly. Ovidiu From owner-chemistry@ccl.net Wed Jan 2 22:39:01 2008 From: "Mohamed M Ahmida mahmida||gmail.com" To: CCL Subject: CCL:G: Error on pcm-TD-DFT calculation on G03 Message-Id: <-35970-080102193719-30063-jbfNAMLfSI56+91Euys0Aw%server.ccl.net> X-Original-From: "Mohamed M Ahmida" Date: Wed, 2 Jan 2008 19:37:15 -0500 Sent to CCL by: "Mohamed M Ahmida" [mahmida~!~gmail.com] Pleas anybody faced the same error as me: AdVTs1: ISph= 407 is engulfed by JSph= 408 but Ae( 407) is not yet zero! Error termination via Lnk1e in /usr/local/src/g03/l301.exe at Sun Dec 23 10:06:43 2007. Job cpu time: 4 days 17 hours 59 minutes 57.1 seconds. File lengths (MBytes): RWF= 1019 Int= 0 D2E= 0 Chk= 51 Scr= 1 Many thanks From owner-chemistry@ccl.net Wed Jan 2 23:14:01 2008 From: "Steve Bowlus chezbowlus]=[comcast.net" To: CCL Subject: CCL:G: what program can calculate the electrical properties of polymers Message-Id: <-35971-080102224704-18766-qHW0w21DN6Ce71lc+xnEkw:_:server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 02 Jan 2008 19:46:04 -0800 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus-,-comcast.net] The Virtual NanoLab from Atomistix might be able to do some of these calculations. Good Luck, Steve > Sent to CCL by: "Wei WANG" [wangwei[a]ciac.jl.cn] > > Dear CCLers, > > Could you please advice me what program can calculate the > electrical properties of polymers, especially the high polymers? > The electrical properties of polymers refers to the behavior and > the various physical phenomena of polymers under the externally > applied electric field, such as polarizations, dielectric > constants, dielectric losses, dielectric breakdowns, dielectric > strengths, electrostatic phenomena, conductivities. We have been > doing experiments mainly on the high polymers films, and at > present we are trying to do some calculations. Could you please > tell me what program can calculate one or some of the electrical > properties of polymers? Whether the Gaussian 03 program can > calculate the polymers' electrical properties or not? > > Best regards, > > Wei WANG > > > > E-mail to subscribers: CHEMISTRY^^ccl.net > or use: > > > E-mail to administrators: > > CHEMISTRY-REQUEST^^ccl.net > or use> > Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > > > > > > > -- > ---- ___ ___ ___ > /\ \ /\ \ /\ \ > /::\ \ /::\ \ \:\ \ > Diego Moreno /:/\:\__\\:\:\__\ /::\__\ > \:\:\/__/ \::/ //:/\/__/ > Grupo de Química Teórica \::/ / /:/ / \/__/ > Universidad Nacional de Col. \/__/ \/__/