From owner-chemistry@ccl.net Tue Jun 30 04:26:01 2009 From: "Barry Hardy barry.hardy .. vtxmail.ch" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39653-090630035245-14354-NWNTFH34voZ5sO6eL7LqHA(-)server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 30 Jun 2009 08:52:22 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy(a)vtxmail.ch] Hi Rick! An interesting new development will be the phase 2 of the US EPA ToxCast program which will evaluate toxicities of many existing chemicals and drugs. Also Pfizer has agreed to make public clinical data on more than 100 drugs that showed adverse effects in clinical human testing, so that the EPA can run the compounds through ToxCast: http://www.epa.gov/ncct/articles/toxcast_summit_release.html http://www.epa.gov/ncct/toxcast/ best regards Barry Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (http://www.opentox.org/) Douglas Connect LLC, Switzerland Email: barry.hardy -(at)- douglasconnect.com Tel: +41 61 851 0170 Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov wrote: > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov] > It should also be noted that some lead compounds and others investigated may not be public knowledge; drug companies do not have to release information about molecules they've made and studied unless they wish to put one of them on the market. Certainly, the FDA gets involved before human tests are conducted, but if the drug never goes to market, it's chemical structure and biological action do not become public knowledge. That information is regarded as confidential trade secrets, owned by the company that developed it. > > -- > Rick Venable 5635FL/T906 > Membrane Biophysics Section > NIH/NHLBI Lab. of Computational Biology > Bethesda, MD 20892-9314 U.S.A. > (301) 496-1905 venabler AT nhlbi*nih*gov > > > > > On 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu" wrote: > > > > Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu] > One approach is to use Chemical Abstract's SciFinder Scholar. Enter the > drug, request the references and filter for articles that describe the > synthesis or early pharmacological evaluation. If you are lucky, you > will find the desired journal article. Otherwise, it probably is buried > in the patent literature. > > John Block > > John H. Block Phone: 541-737-5779 > College of Pharmacy Fax: 541-737-3999 > Oregon State University > Corvallis, OR 97331 > John.Block : oregonstate.edu > blockj : onid.orst.edu > > -----Original Message----- > >> From: owner-chemistry+john.block==orst.edu : ccl.net >> > [mailto:owner-chemistry+john.block==orst.edu : ccl.net] On Behalf Of > Jeremy Besnard j10b84%a%hotmail.com > Sent: Monday, June 29, 2009 2:15 AM > To: Block, John H. > Subject: CCL: Find a lead from a drug > > > Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] > Dear colleagues, > > I have a list of drugs which are on the market and I'd like to find the > lead compound which was used as starting point for the lead optimization > process. > > But the artciles related a story of a drug are not easy to find. An easy > one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 > Inhibitor. 2: > 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione > Analogues. But by looking for name of drug + discovery in a search > engine I don't get hits. I also tried with lead, SAR... > > I'd like to know if you have some hints and tips to help find a lead > with the name of the drug. Also if you know a relatively recent set of > leads and drugs that could be very useful. > > Thank you. > > Jeremy=Job: http://www.ccl.net/jobs-=is is automatically added to each message by the mailing script =http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -=his is automatically added to each message by the mailing script =-> > > > From owner-chemistry@ccl.net Tue Jun 30 07:03:00 2009 From: "Pavle Mocilac pavle.mocilac2..mail.dcu.ie" To: CCL Subject: CCL:G: Free Gibbs energy... Message-Id: <-39654-090630060732-20602-y5b7V/ULBD9myz8aGrzN/g*server.ccl.net> X-Original-From: Pavle Mocilac Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=iso-8859-1 Date: Tue, 30 Jun 2009 10:25:34 +0100 MIME-Version: 1.0 Sent to CCL by: Pavle Mocilac [pavle.mocilac2|,|mail.dcu.ie] Re: CCL: Free Gibbs energy...

Dear Pedro 


Thank you for the tips


I found a nice piece of work in here 


Theoretical prediction of relative and absolute pK(a) values of aminopyridines 

Author(s): Caballero NA, Melendez FJ, Munoz-Cara C, et al.

Source: BIOPHYSICAL CHEMISTRY  Volume: 124   Issue: 2   Pages: 155-160   Published: NOV 20 2006 


The authors were using gas phase and solvated forms of molecules, and G1 method for calculation of deltaGs.

But it was not so clear to me where is the G value in Gaussian output (since I'm a Gaussian newbie). I tried the same with B3LYP/6-311G++ but it seems to me that usage of compound methods like G1, G2, CBS-Q etc is must in this case, since my pKa values were wrong.   




Best regards,


Pavle Mocilac


============================================

Pavle Mocilac

Postgraduate Researcher

T3 - Targeted Therapeutics and Theranostics

Room X249, School of Chemistry

Dublin City University

Dublin 9, Dublin, Ireland

mobile: +353872167022

mailto:pavle.mocilac2|mail.dcu.ie

============================================

Monday, June 29, 2009, 11:23:11 PM, you wrote:

The line you are interested in is the one labelled:



>  Sum of electronic and thermal Free Energies=         -303.561504


Get those lines from the output files on the acid and baisc forms. Then subtract them and convert the values from hartree to kJ.mol-1 (the conversion factor is approximately 627.51*4.184)

Then convert the energies to pKa using the DeltaG=-RT ln K


Remember that the computed values are gas phase ones.... In solution you have to take account of solvation of both forms AND solvation of the proton.


Cheers!

Pedro


-- 

Pedro J. Silva

Assistant Professor

Universidade Fernando Pessoa

Porto - Portugal

http://www2.ufp.pt/~pedros/science/science.htm
From owner-chemistry@ccl.net Tue Jun 30 08:01:01 2009 From: "Aditya Khandavelli svk003 ~ latech.edu" To: CCL Subject: CCL: Problem in TD-DFT calculations- please help Message-Id: <-39655-090629190700-4215-Wp0zZtjOxSZu+UImE0Kung(-)server.ccl.net> X-Original-From: "Aditya Khandavelli" Date: Mon, 29 Jun 2009 19:06:56 -0400 Sent to CCL by: "Aditya Khandavelli" [svk003^latech.edu] Dear All, I'm working on TD-DFT calculations. I encountered an error while running a calculation. It is as follows, ** ERROR IN INITNF. NUMBER OF VARIABLES ( 69) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** My input is as follows "#P TD=(root=1) b3lyp Test opt=maxcycle=1024 Freq scfcyc=1024". I've used two different basis sets for my calculation as my calculation involves transition metal. I'm using LOS-ALAMOS basis set for the transition metal atoms and 6-31+G(D) basis set for the other atoms, Which i've declared after the Z-Matrix. Kindly, help me out in fixing this error. regards, Aditya Khandavelli. From owner-chemistry@ccl.net Tue Jun 30 09:33:01 2009 From: "Loan Huynh huynhkl2000\a/yahoo.ca" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39656-090630093122-9512-QEJdciRoC8MpcnAohxxw3A|-|server.ccl.net> X-Original-From: Loan Huynh Content-Type: multipart/alternative; boundary="0-61614328-1246365067=:49624" Date: Tue, 30 Jun 2009 05:31:07 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000() yahoo.ca] --0-61614328-1246365067=:49624 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi CLLers, I would like to know approximately how many software's for evaluating toxic= ities of drugs.=A0 Which one is more reliable?=A0=20 Thanks, Loan=20 --- On Tue, 6/30/09, Barry Hardy barry.hardy .. vtxmail.ch wrote: > From: Barry Hardy barry.hardy .. vtxmail.ch Subject: CCL: Find a lead from a drug To: "Huynh, Loan " Received: Tuesday, June 30, 2009, 2:52 AM Sent to CCL by: Barry Hardy [barry.hardy(a)vtxmail.ch] Hi Rick! An interesting new development will be the phase 2 of the US EPA ToxCast=20 program which will evaluate toxicities of many existing chemicals and=20 drugs.=A0 Also Pfizer has agreed to make public clinical data on more than= =20 100 drugs that showed adverse effects in clinical human testing, so that=20 the EPA can run the compounds through ToxCast: http://www.epa.gov/ncct/articles/toxcast_summit_release.html http://www.epa.gov/ncct/toxcast/ best regards Barry Barry Hardy PhD Director, Community of Practice & Research Activities and OpenTox Project Coordinator (http://www.opentox.org/) Douglas Connect LLC, Switzerland Email: barry.hardy -(at)- douglasconnect.com Tel: +41 61 851 0170 Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov wrote: > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.= gov] > It should also be noted that some lead compounds and others investigated = may not be public knowledge; drug companies do not have to release informat= ion about molecules they've made and studied unless they wish to put one of= them on the market.=A0 Certainly, the FDA gets involved before human tests= are conducted, but if the drug never goes to market, it's chemical structu= re and biological action do not become public knowledge.=A0 That informatio= n is regarded as confidential trade secrets, owned by the company that deve= loped it. > > -- > Rick Venable=A0 =A0 =A0 5635FL/T906 > Membrane Biophysics Section > NIH/NHLBI Lab. of Computational Biology > Bethesda, MD=A0 20892-9314=A0=A0=A0U.S.A. > (301) 496-1905=A0=A0=A0venabler AT nhlbi*nih*gov > > > > > On 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu" wrote: > > > > Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu] > One approach is to use Chemical Abstract's SciFinder Scholar.=A0 Enter th= e > drug, request the references and filter for articles that describe the > synthesis or early pharmacological evaluation.=A0 If you are lucky, you > will find the desired journal article.=A0 Otherwise, it probably is burie= d > in the patent literature. > > John Block > > John H. Block=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Phone:=A0 541-737-57= 79 > College of Pharmacy=A0 =A0 =A0 =A0=A0=A0Fax:=A0 =A0 =A0 541-737-3999 > Oregon State University > Corvallis, OR 97331 > John.Block : oregonstate.edu > blockj : onid.orst.edu > > -----Original Message----- >=A0=A0=A0 >> From: owner-chemistry+john.block=3D=3Dorst.edu : ccl.net >>=A0 =A0=A0=A0 > [mailto:owner-chemistry+john.block=3D=3Dorst.edu : ccl.net] On Behalf Of > Jeremy Besnard j10b84%a%hotmail.com > Sent: Monday, June 29, 2009 2:15 AM > To: Block, John H. > Subject: CCL: Find a lead from a drug > > > Sent to CCL by: "Jeremy=A0 Besnard" [j10b84[-]hotmail.com] > Dear colleagues, > > I have a list of drugs which are on the market and I'd like to find the > lead compound which was used as starting point for the lead optimization > process. > > But the artciles related a story of a drug are not easy to find. An easy > one is The Discovery of Tadalafil:=A0 A Novel and Highly Selective PDE5 > Inhibitor. 2: > 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione > Analogues. But by looking for name of drug + discovery in a search > engine I don't get hits. I also tried with lead, SAR... > > I'd like to know if you have some hints and tips to help find a lead > with the name of the drug. Also if you know a relatively recent set of > leads and drugs that could be very useful. > > Thank you. > > Jeremy=3DJob: http://www.ccl.net/jobs-=3Dis is automatically added to eac= h message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_= messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spamm= ers.txt > > > -=3Dhis is automatically added to each message by the mailing script =3D-= > > > > -=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 ____________________________________________________________= ______=0ALooking for the perfect gift? Give the gift of Flickr! =0A=0Ahttp:= //www.flickr.com/gift/ --0-61614328-1246365067=:49624 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi CLLers,

I would like to know approx= imately how many software's for evaluating toxicities of drugs.  Which= one is more reliable? 

Thanks,
Loan

--- On Tue,= 6/30/09, Barry Hardy barry.hardy .. vtxmail.ch <owner-chemistry*_*ccl.= net> wrote:

From: Barry Hardy ba= rry.hardy .. vtxmail.ch <owner-chemistry*_*ccl.net>
Subject: CCL: Fi= nd a lead from a drug
To: "Huynh, Loan " <huynhkl2000*_*yahoo.ca= >
Received: Tuesday, June 30, 2009, 2:52 AM


Sent to CCL by: Barry Hardy [barry.hardy(a)vtxmail.ch]
Hi Ric= k!

An interesting new development will be the phase 2 of the US EPA = ToxCast
program which will evaluate toxicities of many existing chemica= ls and
drugs.  Also Pfizer has agreed to make public clinical data on mo= re than
100 drugs that showed adverse effects in clinical human testing= , so that
the EPA can run the compounds through ToxCast:

http://www.epa.gov/ncct/articles/toxcast_summit_release.html
http:/= /www.epa.gov/ncct/toxcast/

best regards
Barry


Barr= y Hardy PhD
Director, Community of Practice & Research Activitiesand OpenTox Project Coordinator (http://www.opentox.org/)
Douglas Connect LLC, Switzerla= nd
Email: barry.hardy -(at)- douglasconnect.com
Tel: +41 61 851 0170<= br>

Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov wrote:<= br>> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov]
> It should also be noted that some lead = compounds and others investigated may not be public knowledge; drug compani= es do not have to release information about molecules they've made and stud= ied unless they wish to put one of them on the market.  Certainly, the= FDA gets involved before human tests are conducted, but if the drug never = goes to market, it's chemical structure and biological action do not become= public knowledge.  That information is regarded as confidential trade= secrets, owned by the company that developed it.
>
> --
>= ; Rick Venable      5635FL/T906
> Membrane Biophysics = Section
> NIH/NHLBI Lab. of Computational Biology
> Bethesda, M= D  20892-9314   U.S.A.
> (301) 496-1905 &nbs= p; venabler AT nhlbi*nih*gov
>
>
>
>
> O= n 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu" <owner-chemistry..ccl.net> wrote:
>
>
>
> Se= nt to CCL by: "Block, John" [john.block.:.oregonstate.edu]
> One appr= oach is to use Chemical Abstract's SciFinder Scholar.  Enter the
&g= t; drug, request the references and filter for articles that describe the> synthesis or early pharmacological evaluation.  If you are luck= y, you
> will find the desired journal article.  Otherwise, it p= robably is buried
> in the patent literature.
>
> John Bl= ock
>
> John H. Block            =         Phone:  541-737-5779
> College of Ph= armacy         Fax:      541-7= 37-3999
> Oregon State University
> Corvallis, OR 97331
>= John.Block : oregonstate.edu
> blockj : onid.orst.edu
>
>= ; -----Original Message-----
>   
>> From: owner-chemistry+john.block=3D=3Dorst.edu : ccl.net
>> =    
> [mailto:owner-chemistry+john.block=3D=3Dorst.ed= u : ccl.net] On Behalf Of
> Jeremy Besnard j10b84%a%hotmail.com
&g= t; Sent: Monday, June 29, 2009 2:15 AM
> To: Block, John H.
> S= ubject: CCL: Find a lead from a drug
>
>
> Sent to CCL by= : "Jeremy  Besnard" [j10b84[-]hotmail.com]
> Dear colleagues,>
> I have a list of drugs which are on the market and I'd like t= o find the
> lead compound which was used as starting point for the l= ead optimization
> process.
>
> But the artciles related = a story of a drug are not easy to find. An easy
> one is The Discover= y of Tadalafil:  A Novel and Highly Selective PDE5
> Inhibitor. = 2:
> 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4= -dione
> Analogues. But by looking for name of drug + discovery in a search
> engine I don't get hits. I also tried with lead, SAR...
= >
> I'd like to know if you have some hints and tips to help find = a lead
> with the name of the drug. Also if you know a relatively rec= ent set of
> leads and drugs that could be very useful.
>
&g= t; Thank you.
>
> Jeremy=3DJob: http://www.ccl.net/jobs-=3Dis is automatic= ally added to each message by the mailing script =3Dhttp://www.ccl.net/c= gi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp= ://www.ccl.net/spammers.txt
>
>
> -=3Dhis is automati= cally added to each message by the mailing script =3D->
>
><= br>>



-=3D This is automatically added to each message by = the mailing script =3D-
To recover the email address of the author of the message, = please change
the strange characters on the top line to the *_* sign. You = can also
E-= mail to subscribers: CHEMISTRY*_*ccl.net or use:
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E-ma= il to administrators: CHEMISTRY-REQUEST*_*ccl.net or use
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= Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br>
Search Messages: http://www.ccl.net/chemistry/searchccl/index.= shtml
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RTFI: http://www.= ccl.net/chemistry/aboutccl/instructions/


=

=0A
Get the name you've always wanted ! *_*ymail.= com or *_*rocketmail.com. --0-61614328-1246365067=:49624-- From owner-chemistry@ccl.net Tue Jun 30 11:05:01 2009 From: "Barry Hardy barry.hardy ~ vtxmail.ch" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39657-090630105806-10487-5uyWPV54/ggZpcqh5V1YNA^server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 30 Jun 2009 16:57:43 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy,,vtxmail.ch] Sorry, Jim, I don't know the exact answer to this question, and on timing, but perhaps someone on the list can clarify (?). Barry James T Metz wrote: > > Barry, > > Has Pfizer made their structures and data available yet? If > so, what is the HTML link? > > Thank you. > > Regards, > Jim Metz > > > James T. Metz, Ph.D. > Research Investigator Chemist > > GPRD R4DG AP10-LL04H > Abbott Laboratories > 100 Abbott Park Road > Abbott Park, IL 60064-6100 > U.S.A. > > Office (847) 936 - 0441 > FAX (847) 935 - 0548 > > james.metz*abbott.com > > This communication may contain information that is legally privileged, > confidential, or exempt from disclosure. If you are not the intended > recipient, please note that any dissemination, distribution, use, or > copying of this communication is strictly prohibited. Anyone who > receives this message in error should notify the sender immediately by > telephone (847 - 936 - 0441) or return email and delete it from his or > her computer. > > > *"Barry Hardy barry.hardy .. vtxmail.ch" * > Sent by: owner-chemistry+james.metz==abbott.com*ccl.net > > 06/30/2009 01:52 AM > Please respond to > "CCL Subscribers" > > > > To > "Metz, Jim " > cc > > Subject > CCL: Find a lead from a drug > > > > > > > > > > > Sent to CCL by: Barry Hardy [barry.hardy(a)vtxmail.ch] > Hi Rick! > > An interesting new development will be the phase 2 of the US EPA ToxCast > program which will evaluate toxicities of many existing chemicals and > drugs. Also Pfizer has agreed to make public clinical data on more than > 100 drugs that showed adverse effects in clinical human testing, so that > the EPA can run the compounds through ToxCast: > > http://www.epa.gov/ncct/articles/toxcast_summit_release.html > > http://www.epa.gov/ncct/toxcast/ > > best regards > Barry > > > Barry Hardy PhD > Director, Community of Practice & Research Activities > and OpenTox Project Coordinator (http://www.opentox.org/) > Douglas Connect LLC, Switzerland > Email: barry.hardy -(at)- douglasconnect.com > Tel: +41 61 851 0170 > > > Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov wrote: > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" > [venabler#%#nhlbi.nih.gov] > > It should also be noted that some lead compounds and others > investigated may not be public knowledge; drug companies do not have > to release information about molecules they've made and studied unless > they wish to put one of them on the market. Certainly, the FDA gets > involved before human tests are conducted, but if the drug never goes > to market, it's chemical structure and biological action do not become > public knowledge. That information is regarded as confidential trade > secrets, owned by the company that developed it. > > > > -- > > Rick Venable 5635FL/T906 > > Membrane Biophysics Section > > NIH/NHLBI Lab. of Computational Biology > > Bethesda, MD 20892-9314 U.S.A. > > (301) 496-1905 venabler AT nhlbi*nih*gov > > > > > > > > > > On 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu" > wrote: > > > > > > > > Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu] > > One approach is to use Chemical Abstract's SciFinder Scholar. Enter the > > drug, request the references and filter for articles that describe the > > synthesis or early pharmacological evaluation. If you are lucky, you > > will find the desired journal article. Otherwise, it probably is buried > > in the patent literature. > > > > John Block > > > > John H. Block Phone: 541-737-5779 > > College of Pharmacy Fax: 541-737-3999 > > Oregon State University > > Corvallis, OR 97331 > > John.Block : oregonstate.edu > > blockj : onid.orst.edu > > > > -----Original Message----- > > > >> From: owner-chemistry+john.block==orst.edu : ccl.net > >> > > [mailto:owner-chemistry+john.block==orst.edu : ccl.net] On Behalf Of > > Jeremy Besnard j10b84%a%hotmail.com > > Sent: Monday, June 29, 2009 2:15 AM > > To: Block, John H. > > Subject: CCL: Find a lead from a drug > > > > > > Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] > > Dear colleagues, > > > > I have a list of drugs which are on the market and I'd like to find the > > lead compound which was used as starting point for the lead optimization > > process. > > > > But the artciles related a story of a drug are not easy to find. An easy > > one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 > > Inhibitor. 2: > > 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione > > Analogues. But by looking for name of drug + discovery in a search > > engine I don't get hits. I also tried with lead, SAR... > > > > I'd like to know if you have some hints and tips to help find a lead > > with the name of the drug. Also if you know a relatively recent set of > > leads and drugs that could be very useful. > > > > Thank you. > > > > Jeremy=Job: http://www.ccl.net/jobs-=is is automatically added to > each message by the mailing script > =http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Tue Jun 30 11:42:00 2009 From: "Aniko Simon aniko---simbiosys.ca" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39658-090630110806-13089-QD1Yd4yUu67JmcAp0LkI7A~!~server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 30 Jun 2009 11:08:02 -0400 Sent to CCL by: "Aniko Simon" [aniko{:}simbiosys.ca] Hi Loan, EPA used eHiTS from SimBioSys as one of the software tools for toxicity screening in Phase I of the ToxCast project cited by Barry, here is our press release: http://www.simbiosys.ca/whatsnew/news/pressrel_2007.html#20071105 There is some more recent information about the screening process here: http://www.epa.gov/NCCT/sot/posters/2009/24_JRabinowitz_SOT09.pdf best regards, Aniko On June 30, 2009, Loan Huynh huynhkl2000a/yahoo.ca wrote: > Hi CLLers, > > I would like to know approximately how many software's for evaluating > toxicities of drugs. Which one is more reliable? > > Thanks, > Loan > > --- On Tue, 6/30/09, Barry Hardy barry.hardy .. vtxmail.ch wrote: > > From: Barry Hardy barry.hardy .. vtxmail.ch > > Subject: CCL: Find a lead from a drug > To: "Huynh, Loan " > Received: Tuesday, June 30, 2009, 2:52 AM > > > Sent to CCL by: Barry Hardy [barry.hardy(a)vtxmail.ch] > Hi Rick! > > An interesting new development will be the phase 2 of the US EPA ToxCast > program which will evaluate toxicities of many existing chemicals and > drugs. Also Pfizer has agreed to make public clinical data on more than > 100 drugs that showed adverse effects in clinical human testing, so that > the EPA can run the compounds through ToxCast: > > http://www.epa.gov/ncct/articles/toxcast_summit_release.html > > http://www.epa.gov/ncct/toxcast/ > > best regards > Barry > > > Barry Hardy PhD > Director, Community of Practice & Research Activities > and OpenTox Project Coordinator (http://www.opentox.org/) > Douglas Connect LLC, Switzerland > Email: barry.hardy -(at)- douglasconnect.com > Tel: +41 61 851 0170 > > Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov wrote: > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" > > [venabler#%#nhlbi.nih.gov] It should also be noted that some lead > > compounds and others investigated may not be public knowledge; drug > > companies do not have to release information about molecules they've made > > and studied unless they wish to put one of them on the market. > > Certainly, the FDA gets involved before human tests are conducted, but if > > the drug never goes to market, it's chemical structure and biological > > action do not become public knowledge. That information is regarded as > > confidential trade secrets, owned by the company that developed it. > > > > -- > > Rick Venable 5635FL/T906 > > Membrane Biophysics Section > > NIH/NHLBI Lab. of Computational Biology > > Bethesda, MD 20892-9314 U.S.A. > > (301) 496-1905 venabler AT nhlbi*nih*gov > > > > > > > > > > On 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu" > > wrote: > > > > > > > > Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu] > > One approach is to use Chemical Abstract's SciFinder Scholar. Enter the > > drug, request the references and filter for articles that describe the > > synthesis or early pharmacological evaluation. If you are lucky, you > > will find the desired journal article. Otherwise, it probably is buried > > in the patent literature. > > > > John Block > > > > John H. Block Phone: 541-737-5779 > > College of Pharmacy Fax: 541-737-3999 > > Oregon State University > > Corvallis, OR 97331 > > John.Block : oregonstate.edu > > blockj : onid.orst.edu > > > > -----Original Message----- > > > > > >> From: owner-chemistry+john.block==orst.edu : ccl.net > >> > > > > [mailto:owner-chemistry+john.block==orst.edu : ccl.net] On Behalf Of > > Jeremy Besnard j10b84%a%hotmail.com > > Sent: Monday, June 29, 2009 2:15 AM > > To: Block, John H. > > Subject: CCL: Find a lead from a drug > > > > > > Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] > > Dear colleagues, > > > > I have a list of drugs which are on the market and I'd like to find the > > lead compound which was used as starting point for the lead optimization > > process. > > > > But the artciles related a story of a drug are not easy to find. An easy > > one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 > > Inhibitor. 2: > > 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione > > Analogues. But by looking for name of drug + discovery in a search > > engine I don't get hits. I also tried with lead, SAR... > > > > I'd like to know if you have some hints and tips to help find a lead > > with the name of the drug. Also if you know a relatively recent set of > > leads and drugs that could be very useful. > > > > Thank you. >> > > Jeremy From owner-chemistry@ccl.net Tue Jun 30 12:36:01 2009 From: "James Robinson james.robinson : prosonix.co.uk" To: CCL Subject: CCL: Find a lead drug, toxicity etc.. Message-Id: <-39659-090630123005-6211-xOhILuT4mDVbU8zQKD0/gA-*-server.ccl.net> X-Original-From: "James Robinson" Date: Tue, 30 Jun 2009 12:30:01 -0400 Sent to CCL by: "James Robinson" [james.robinson^-^prosonix.co.uk] Hi ccler's, Some people user qsar/qspr studies to evaluate P450 cytochrmoe character and Caco2 character guesses to in-silico screen lead candidates. James Senior Scientist Prosonix Ltd, Oxford. From owner-chemistry@ccl.net Tue Jun 30 14:40:01 2009 From: "Kalju Kahn kalju~~chem.ucsb.edu" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39660-090630141727-30664-YEkwq8kAyWsiojjstlR87A\a/server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 30 Jun 2009 11:17:12 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju\a/chem.ucsb.edu] Jeremy, One thing to keep in mind is that the current drug name most likely did not exist when it was developed from the lead. Thus, searching by the current name may not yield much about the early history. You will have a better luck after finding out what was the corporate code for this drug. For example, just last month I sat down with one of the best students in our "drug design" class. He was unable to find any SciFinder references about development and pharmacokinetic studies on brequinar (dihydroorotate dehydrogenase inhibitor). However, by reading the titles of references cited in "brequinar" papers, we found out that the drug was called DuP 785 in the early stages of development; search for DuP 785 turned up what he needed. Hope this helps, Kalju > Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] > Dear colleagues, > > I have a list of drugs which are on the market and I'd like to find the > lead compound which was used as starting point for the lead optimization > process. > > But the artciles related a story of a drug are not easy to find. An easy > one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 > Inhibitor. 2: > 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4-dione > Analogues. But by looking for name of drug + discovery in a search > engine I don't get hits. I also tried with lead, SAR... > > I'd like to know if you have some hints and tips to help find a lead > with the name of the drug. Also if you know a relatively recent set of > leads and drugs that could be very useful. > > Thank you. > > Jeremy > > > > -= This is automatically added to each message by the mailing script > =-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Tue Jun 30 15:14:00 2009 From: "Babak Khalili khalili.babak .. gmail.com" To: CCL Subject: CCL: To make a PDB file Message-Id: <-39661-090630145738-9699-54OHvRb21vupUHAveBdydg%server.ccl.net> X-Original-From: Babak Khalili Content-Type: multipart/alternative; boundary=001636c5a82f8c4221046d95091f Date: Tue, 30 Jun 2009 23:03:01 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak]~[gmail.com] --001636c5a82f8c4221046d95091f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear subscribers, I design a new molecule based on amino acid blocks and now I would like to make a PDB format file, to do other calculations. Saving the file with the command of file save as, pdb. in Chem3D can not help me because the PDB format is nor realiable. You will be so appreciated to help me to make the related PDB file.. Sincerely, Babak Khalili, PhD candidate of Biochemistry --001636c5a82f8c4221046d95091f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear subscribers,

I design a new molecule based on amino acid blocks= and now I would like to make a PDB format file, to do other calculations. = Saving the file with the command of file save as, pdb. in Chem3D can not he= lp me=A0 because the PDB format is nor realiable. You will be so appreciate= d to help me to make the related PDB file..

Sincerely,
Babak Khalili,
PhD candidate of Biochemistry
--001636c5a82f8c4221046d95091f-- From owner-chemistry@ccl.net Tue Jun 30 18:54:00 2009 From: "Chris Swain swain]~[mac.com" To: CCL Subject: CCL: Find a lead from a drug Message-Id: <-39662-090630141233-30032-4RlLy+AQbCub5wbwZT6Myw]-[server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Boundary_(ID_kl0LK6WZ+38KnKo3KuKCLA)" Date: Tue, 30 Jun 2009 11:36:42 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain%x%mac.com] --Boundary_(ID_kl0LK6WZ+38KnKo3KuKCLA) Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-transfer-encoding: 7BIT Have a look at Drug Prototypes and Their Exploitation by Walter Sneader, John Wiley & Sons Ltd, ISBN-10: 0471948470 Chris Dr Chris Swain BA MA (Cantab) PhD CChem FRSC Cambridge MedChem Consulting, 8 Mangers Lane, Duxford, Cambs, United Kingdom CB22 4RN. swain]![mac.com http://www.cambridgemedchemconsulting.com On 30 Jun 2009, at 07:52, Barry Hardy barry.hardy .. vtxmail.ch wrote: > > Sent to CCL by: Barry Hardy [barry.hardy(a)vtxmail.ch] > Hi Rick! > > An interesting new development will be the phase 2 of the US EPA > ToxCast program which will evaluate toxicities of many existing > chemicals and drugs. Also Pfizer has agreed to make public clinical > data on more than 100 drugs that showed adverse effects in clinical > human testing, so that the EPA can run the compounds through ToxCast: > > http://www.epa.gov/ncct/articles/toxcast_summit_release.html > > http://www.epa.gov/ncct/toxcast/ > > best regards > Barry > > > Barry Hardy PhD > Director, Community of Practice & Research Activities > and OpenTox Project Coordinator (http://www.opentox.org/) > Douglas Connect LLC, Switzerland > Email: barry.hardy -(at)- douglasconnect.com > Tel: +41 61 851 0170 > > > Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov wrote: >> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler# >> %#nhlbi.nih.gov] >> It should also be noted that some lead compounds and others >> investigated may not be public knowledge; drug companies do not >> have to release information about molecules they've made and >> studied unless they wish to put one of them on the market. >> Certainly, the FDA gets involved before human tests are conducted, >> but if the drug never goes to market, it's chemical structure and >> biological action do not become public knowledge. That information >> is regarded as confidential trade secrets, owned by the company >> that developed it. >> >> -- >> Rick Venable 5635FL/T906 >> Membrane Biophysics Section >> NIH/NHLBI Lab. of Computational Biology >> Bethesda, MD 20892-9314 U.S.A. >> (301) 496-1905 venabler AT nhlbi*nih*gov >> >> >> >> >> On 6/29/09 1:36 PM, "Block, John john.block() oregonstate.edu" >> wrote: >> >> >> >> Sent to CCL by: "Block, John" [john.block.:.oregonstate.edu] >> One approach is to use Chemical Abstract's SciFinder Scholar. >> Enter the >> drug, request the references and filter for articles that describe >> the >> synthesis or early pharmacological evaluation. If you are lucky, you >> will find the desired journal article. Otherwise, it probably is >> buried >> in the patent literature. >> >> John Block >> >> John H. Block Phone: 541-737-5779 >> College of Pharmacy Fax: 541-737-3999 >> Oregon State University >> Corvallis, OR 97331 >> John.Block : oregonstate.edu >> blockj : onid.orst.edu >> >> -----Original Message----- >> >>> From: owner-chemistry+john.block==orst.edu : ccl.net >>> >> [mailto:owner-chemistry+john.block==orst.edu : ccl.net] On Behalf Of >> Jeremy Besnard j10b84%a%hotmail.com >> Sent: Monday, June 29, 2009 2:15 AM >> To: Block, John H. >> Subject: CCL: Find a lead from a drug >> >> >> Sent to CCL by: "Jeremy Besnard" [j10b84[-]hotmail.com] >> Dear colleagues, >> >> I have a list of drugs which are on the market and I'd like to find >> the >> lead compound which was used as starting point for the lead >> optimization >> process. >> >> But the artciles related a story of a drug are not easy to find. An >> easy >> one is The Discovery of Tadalafil: A Novel and Highly Selective PDE5 >> Inhibitor. 2: >> 2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole-1,4- >> dione >> Analogues. But by looking for name of drug + discovery in a search >> engine I don't get hits. I also tried with lead, SAR... >> >> I'd like to know if you have some hints and tips to help find a lead >> with the name of the drug. Also if you know a relatively recent set >> of >> leads and drugs that could be very useful. >> >> Thank you. >> >> Jeremy=Job: http://www.ccl.net/jobs-=is is automatically added to >> each message by the mailing script =http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt >> >> >> -=his is automatically added to each message by the mailing script >> =-> >> >> >> > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/sub_unsub.shtml> > --Boundary_(ID_kl0LK6WZ+38KnKo3KuKCLA) Content-type: text/html; charset=US-ASCII Content-transfer-encoding: quoted-printable Have a look = at

Drug Prototypes and Their Exploitation = by John Wiley & Sons Ltd, ISBN-10: = 0471948470 

Chris


Dr Chris Swain = BA MA (Cantab) PhD CChem FRSC
Cambridge MedChem = Consulting,
8 Mangers = Lane,
Duxford,
Cambs,
United = Kingdom
CB22 4RN.

On 30 Jun 2009, at 07:52, = Barry Hardy barry.hardy .. vtxmail.ch wrote:


Sent to CCL by: Barry Hardy = [barry.hardy(a)vtxmail.ch]
Hi Rick!

An interesting new = development will be the phase 2 of the US EPA ToxCast program which will = evaluate toxicities of many existing chemicals and drugs.  Also = Pfizer has agreed to make public clinical data on more than 100 drugs = that showed adverse effects in clinical human testing, so that the EPA = can run the compounds through ToxCast:

http= ://www.epa.gov/ncct/articles/toxcast_summit_release.html

http:/= /www.epa.gov/ncct/toxcast/

best regards
Barry


Barry = Hardy PhD
Director, Community of Practice & Research = Activities
and OpenTox Project Coordinator = (http://www.opentox.org/)
Douglas Connect LLC, Switzerland
Email: = barry.hardy -(at)- douglasconnect.com
Tel: +41 61 851 = 0170


Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov = wrote:
Sent to CCL by: "Venable, Richard = (NIH/NHLBI) [E]" [venabler#%#nhlbi.nih.gov]
It should also be noted that some lead compounds and = others investigated may not be public knowledge; drug companies do not = have to release information about molecules they've made and studied = unless they wish to put one of them on the market.  Certainly, the = FDA gets involved before human tests are conducted, but if the drug = never goes to market, it's chemical structure and biological action do = not become public knowledge.  That information is regarded as = confidential trade secrets, owned by the company that developed = it.

--
Rick Venable =      5635FL/T906
Membrane Biophysics Section
NIH/NHLBI Lab. of Computational = Biology
Bethesda, MD =  20892-9314   U.S.A.
(301) 496-1905   venabler AT = nhlbi*nih*gov




On 6/29/09 1:36 = PM, "Block, John john.block() oregonstate.edu" = <owner-chemistry..ccl.net> wrote:



Sent to CCL by: = "Block, John" [john.block.:.oregonstate.edu]
One approach is to use Chemical Abstract's SciFinder = Scholar.  Enter the
drug, = request the references and filter for articles that describe = the
synthesis or early = pharmacological evaluation.  If you are lucky, = you
will find the desired = journal article.  Otherwise, it probably is = buried
in the patent = literature.

John = Block

John H. Block =             &n= bsp;      Phone: =  541-737-5779
College of = Pharmacy         Fax: =      541-737-3999
Oregon State University
Corvallis, OR 97331
John.Block : oregonstate.edu
blockj : onid.orst.edu

-----Original = Message-----
=  
From: owner-chemistry+john.block=3D=3Dorst.edu : = ccl.net
=    
[mailto:owner-chemistry+john.block=3D=3Dorst.edu : = ccl.net] On Behalf Of
Jeremy = Besnard j10b84%a%hotmail.com
Sent: Monday, June 29, 2009 2:15 = AM
To: Block, John = H.
Subject: CCL: Find a lead = > from a drug


Sent to CCL by: = "Jeremy  Besnard" = [j10b84[-]hotmail.com]
Dear = colleagues,

I have a list = of drugs which are on the market and I'd like to find = the
lead compound which was = used as starting point for the lead = optimization
process.

But the = artciles related a story of a drug are not easy to find. An = easy
one is The Discovery of = Tadalafil:  A Novel and Highly Selective = PDE5
Inhibitor. = 2:
2,3,6,7,12,12a-hexahydropyrazino[1,2:1,6]pyrido[3,4-b]indole= -1,4-dione
Analogues. But by = looking for name of drug + discovery in a = search
engine I don't get = hits. I also tried with lead, SAR...

I'd like to = know if you have some hints and tips to help find a = lead
with the name of the = drug. Also if you know a relatively recent set = of
leads and drugs that could = be very useful.

Thank = you.

Jeremy=3DJob: = http://www.ccl.net/jobs-=3Dis is automatically added to each message by = the mailing script = =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemi= stry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


-=3Dhis is = automatically added to each message by the mailing script = =3D->






-=3D This is automatically = added to each message by the mailing script =3D-
To recover the email = address of the author of the message, please change
the strange = characters on the top line to the ]![ sign. You can also
look up the = X-Original-From: line in the mail header.

E-mail to subscribers: = CHEMISTRY]![ccl.net or use:
=     http://www.ccl.net/cgi-bin/ccl/send_ccl_message =     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
Before posting, check wait time at: = http://www.ccl.net

Search = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If = your mail bounces from CCL with 5.7.1 error, check:
=     http://www.ccl.net/spammers.txt

RTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/



= --Boundary_(ID_kl0LK6WZ+38KnKo3KuKCLA)-- From owner-chemistry@ccl.net Tue Jun 30 21:52:01 2009 From: "case case.:.biomaps.rutgers.edu" To: CCL Subject: CCL:G: Free Gibbs energy... Message-Id: <-39663-090630135922-11954-Ub3JzeBAgFsxQFm5Y56opA#,#server.ccl.net> X-Original-From: case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 30 Jun 2009 12:53:16 -0400 Mime-Version: 1.0 Sent to CCL by: case [case(~)biomaps.rutgers.edu] On Mon, Jun 29, 2009, Pavle Mocilac pavle.mocilac2!=!mail.dcu.ie wrote: > > I'm trying to calculate pKa for some compounds. I found some interesting > papers about that, but still, I can not find some simple method of > extracting G values from Gaussian output. Gaussian helps in one way, by computing this line: > Sum of electronic and thermal Free Energies= -303.561504 You can take the difference between this value for the acid, and for its conjugate base, then use simple statistical mechanics (see your favorite Phys Chem textbook) to get the free energy of a proton, and do the math. However, please note: 1. pKa is related to the standard free energy of the deprotonation reaction *in solution*, not in the gas phase. You can combine gas-phase numbers with estimates of solvation free energies to get pKa estimates, but this is a much more complex procedure than just doing gas-phase calculations. 2. If you *are* interested in gas-phase acidities, note that (for historical reasons) they are generally reported as reaction enthalpies (not reaction free energies.) So, you would look for the enthalpy output from Gaussian -- but be sure that you understand how Gaussian is putting all the numbers together. To start, study http://gaussian.com/g_tech/g_ur/k_freq.htm (look for "frequency output"), or look at Chap. 4 of "Exploring Chemistry with Electronic Structure Methods." ...good luck....dave case From owner-chemistry@ccl.net Tue Jun 30 23:15:01 2009 From: "Kelly smilin_iis(_)yahoo.com" To: CCL Subject: CCL: To make a PDB file Message-Id: <-39664-090630195821-10103-pn+ZGqAgxEFDqIVJSDK/rA[#]server.ccl.net> X-Original-From: Kelly Content-Type: multipart/alternative; boundary="0-362569089-1246402688=:61414" Date: Tue, 30 Jun 2009 15:58:08 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Kelly [smilin_iis/a\yahoo.com] --0-362569089-1246402688=:61414 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Babak,=0A=0AI have found Vega ZZ useful (and free!) for converting file = formats.=A0=A0=0A=0AIt=A0reads and saves=A0files in a wide range of=A0forma= ts.=0A=0AAlso, the customer service was top notch when i had some issues ru= nning=A0it on one of my machines.=0A=0AYou can try saving your molecule in = .xyz format,=A0then open it in Vega ZZ, double check the connectivity, and = save it as .pdb file.=0A=0AGood luck!=0A=A0=0A=0A=0A-Kelly=0A=A0=0A"Most fo= lks are about as happy as they make up their minds to be."=A0 - Abraham Lin= coln=0A=0A=0A=0A=0A=0A________________________________=0AFrom: Babak Khalil= i khalili.babak .. gmail.com =0ATo: "Theel, Kelly = " =0ASent: Tuesday, June 30, 2009 11:33:01 AM= =0ASubject: CCL: To make a PDB file=0A=0ADear subscribers,=0A=0AI design a = new molecule based on amino acid blocks and now I would like to make a PDB = format file, to do other calculations. Saving the file with the command of = file save as, pdb. in Chem3D can not help me=A0 because the PDB format is n= or realiable. You will be so appreciated to help me to make the related PDB= file..=0A=0ASincerely,=0ABabak Khalili,=0APhD candidate of Biochemistry=0A --0-362569089-1246402688=:61414 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
Hi Babak,
=0A
 
=0A
I ha= ve found Vega ZZ useful (and free!) for converting file formats.  = ;
=0A
 
=0A
It reads and saves files in a = wide range of formats.
=0A
 
=0A
Also, the cust= omer service was top notch when i had some issues running it on one of= my machines.
=0A
 
=0A
You can try saving your mole= cule in .xyz format, then open it in Vega ZZ, double check the connect= ivity, and save it as .pdb file.
=0A
 
=0A
Good luck= !
 
=0A
=0A
= =0A
 
=0A
-Kelly
=0A 
=0A
"Most folks are about as happy as they make up their minds to= be."  - Abraham Lincoln
=0A
 
=0A

=0A

=0A
=0A=
=0AFrom: Babak= Khalili khalili.babak .. gmail.com <owner-chemistry[a]ccl.net>
<= SPAN style=3D"FONT-WEIGHT: bold">To: "Theel, Kelly " <= ;smilin_iis[a]yahoo.com>
Sent: Tuesday, June 30, 2009 11:33:01 AM
Subject: CCL: To make a PDB file

Dear subs= cribers,

I design a new molecule based on amino acid blocks and now = I would like to make a PDB format file, to do other calculations. Saving th= e file with the command of file save as, pdb. in Chem3D can not help me&nbs= p; because the PDB format is nor realiable. You will be so appreciated to h= elp me to make the related PDB file..

Sincerely,
Babak Khalili,PhD candidate of Biochemistry
--0-362569089-1246402688=:61414--