From owner-chemistry@ccl.net Tue Jul 7 03:43:01 2009 From: "neeraj misra neerajmisra++hotmail.com" To: CCL Subject: CCL:G: parameters Message-Id: <-39698-090707034042-29697-YnMH7SrytD1H++CQ9PnXyA]-[server.ccl.net> X-Original-From: "neeraj misra" Date: Tue, 7 Jul 2009 03:40:39 -0400 Sent to CCL by: "neeraj misra" [neerajmisra---hotmail.com] Can we calculate the asymmtery parameters from the Gaussian 03? From owner-chemistry@ccl.net Tue Jul 7 10:07:01 2009 From: "VITORGE Pierre 094605 Pierre.VITORGE^^cea.fr" To: CCL Subject: CCL: pKa calculation of strong acid Message-Id: <-39699-090707043039-20307-yrACO+cqmSAjAsNCasUOFw[#]server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 7 Jul 2009 09:26:15 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE ~ cea.fr] The pKa of a strong acid have no finite value, namely it does not exist. Pierre Vitorge http://www.vitorge.name -----Message d'origine----- De=A0: owner-chemistry+pierre.vitorge=3D=3Dcea.fr,,ccl.net = [mailto:owner-chemistry+pierre.vitorge=3D=3Dcea.fr,,ccl.net] De la part = de Kefa Lu kefa.lu[-]gmail.com Envoy=E9=A0: lundi 6 juillet 2009 09:26 =C0=A0: VITORGE Pierre 094605 Objet=A0: CCL: pKa calculation of strong acid Sent to CCL by: "Kefa Lu" [kefa.lu/a\gmail.com] Hi,all, Does anybody have experience or idea about the pKa calculation of a = strong acid like HCl in water and protein? Thanks. Kefa -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 7 10:41:00 2009 From: "Tomoko Niwa tmk.niwa_-_gmail.com" To: CCL Subject: CCL: Hydrophobicity Message-Id: <-39700-090707072440-22441-+CKpVwiNIjsab6VZTGo7pA^-^server.ccl.net> X-Original-From: Tomoko Niwa Content-Type: multipart/alternative; boundary=000e0cd146787719c0046e1bddc3 Date: Tue, 7 Jul 2009 20:24:25 +0900 MIME-Version: 1.0 Sent to CCL by: Tomoko Niwa [tmk.niwa/a\gmail.com] --000e0cd146787719c0046e1bddc3 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Babak Please check the following papers: Tomoko Sotomatsu-Niwa, Akio Ogino, Evaluation of the hydrophobic parameters of the amino acid side chains of peptides and their application in QSAR and conformational studies, THEOCHEM (1997), 392, 43-54. Reprints are available on request. Hope this helps, Tomoko =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Tomoko Niwa, Ph.D. Research Lab. Nippon Shinyaku Co., Ltd. Nishiohji Hachijo Minami-ku Kyoto, 601 Japan tel 075-321-9047, fax 075-321-9038 t.niwa at.at nippon-shinyaku.co.jp =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 2009/7/7 Babak Khalili khalili.babak:-:gmail.com > Dear al > How can I calculate the hydrophobicity of a peptide? > > Thank you for your earliest attention > Babak khalili Haddad > --000e0cd146787719c0046e1bddc3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Babak
=A0
Please check the following papers:
Tomoko Sotomatsu-Niwa, Akio Ogin= o, Evaluation of the hydrophobic
parameters of the amino acid side chain= s of peptides and their
application in QSAR and conformational studies, = THEOCHEM (1997),
392, 43-54.
=A0
Reprints are available on request.
=A0
Hope this helps,
=A0
Tomoko
=A0
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D
Tomoko Niwa, Ph.D.
Research Lab. Nippon Shinyaku Co.,= Ltd.
Nishiohji Hachijo Minami-ku Kyoto, 601 Japan
tel 075-321-9047, = fax 075-321-9038
t.niwa at.at nippon-shinyaku.co.jp
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D= -=3D-=3D




=A0
2009/7/7 Babak Khalili khalili.babak:-:gmail.com <owner-chemistry%a%ccl.net>
Dear al
How can I calculate t= he hydrophobicity of a peptide?

Thank you for your earliest attentio= n
Babak khalili Haddad

--000e0cd146787719c0046e1bddc3-- From owner-chemistry@ccl.net Tue Jul 7 11:16:01 2009 From: "Dr David N Haney haney{:}edusoft-lc.com" To: CCL Subject: CCL: Hydrophobicity Message-Id: <-39701-090707024207-9372-P/pjNHQHCII3W1Pb8hqCYw_._server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 6 Jul 2009 22:18:24 -0700 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney a edusoft-lc.com] Babak khalili Haddad, HINT from EduSoft, LC has been used extensively for this purpose. http://www.edusoft-lc.com/hint/ There are 2 related programs, HINT TOOLKIT and HINTLOGP. HINT TOOLKIT includes HINTLOGP as well as HINT for Sybyl and source libraries so that you may include HINT calls into your own software. HINTLOGP is a text based code that will calculate LogP values at the atom or molecule level and hydrophobic descriptors for a database of molecules. HINT TOOLKIT has also been used to calculate scores for docked molecules, to study computational titration, to identify key water molecules, for CoMFA analysis, for LOCK and KEY complementarity analysis, and to map protein cavities. Please let me know if you have any questions. On Tue, Jul 07, 2009 at 01:24:35AM +0430, Babak Khalili khalili.babak:-:gmail.com wrote: > Dear al > How can I calculate the hydrophobicity of a peptide? > > Thank you for your earliest attention > Babak khalili Haddad -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney]~[edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Tue Jul 7 11:51:01 2009 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard=ens-lyon.fr" To: CCL Subject: CCL: Gunzipping a Directory Message-Id: <-39702-090707110632-4565-OAAuWJa7i64P8XImzL1jkA-#-server.ccl.net> X-Original-From: "Paul Fleurat-Lessard" Date: Tue, 7 Jul 2009 11:06:28 -0400 Sent to CCL by: "Paul Fleurat-Lessard" [Paul.Fleurat-Lessard*ens-lyon.fr] Hi CCL'ers, This is not strictly speaking Computational, but it just happens that a student of mine has archived his files using: gzip -cr Dir1 >> Dir1.tar.gz According to him, it should be possible to get all files back to a directory by using: gunzip -c Dir1.tar.gz > Dir1 but this does not work. If you gunzip the Dir1.tar.gz file, you only get one file, containing everything and named as the first file of Dir1. (Of course, I _had_ told him to use tar -xvzf Dir1.tar.gz Dir1, but he found the previous scheme on internet.) I looked into the Dir1.tar.gz file with hexdump, and there are all the files together with their name so that it should be possible to extract them separately. Has anyboddy already faced this ? Thanks in advance, Paul. From owner-chemistry@ccl.net Tue Jul 7 13:14:00 2009 From: "Chitra Narayanan chtra{:}eden.rutgers.edu" To: CCL Subject: CCL: FoldTraj - TraDES query! Message-Id: <-39703-090707124659-11756-0+JoP4+mMH46tBI8hzVvvw a server.ccl.net> X-Original-From: Chitra Narayanan Content-Type: multipart/alternative; boundary=0015174c153e4f356a046e205ec6 Date: Tue, 7 Jul 2009 12:46:27 -0400 MIME-Version: 1.0 Sent to CCL by: Chitra Narayanan [chtra{}eden.rutgers.edu] --0015174c153e4f356a046e205ec6 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, I'm trying to use the TraDES program to generate ensembles of unfolded structures. I have problems constraining the system to have specific secondary structural elements (Helix/ sheet) in the different regions of the protein. I'd be grateful if someone with an experience in using constraints (in TraDES) to generate (mostly unstructured) proteins with regional secondary structural bias could help out! Thank you! Chitra --0015174c153e4f356a046e205ec6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 
Hi,

I'm trying to use the TraDES program to generate ensembles of unfolded
structures. I have problems  constraining the system to have specific
secondary structural elements (Helix/ sheet) in the different regions of the


protein.

I'd be grateful if someone with an experience in using constraints (in
TraDES) to generate (mostly unstructured) proteins with regional secondary
structural bias could help out!

Thank you!



Chitra
--0015174c153e4f356a046e205ec6-- From owner-chemistry@ccl.net Tue Jul 7 14:47:00 2009 From: "Wolf Ihlenfeldt wdi*o*xemistry.com" To: CCL Subject: CCL: Gunzipping a Directory Message-Id: <-39704-090707121932-29560-xS4O7mpTks+17w57CgAFfg+/-server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=0016e6d96751107b7b046e1ffc46 Date: Tue, 7 Jul 2009 18:19:18 +0200 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi^xemistry.com] --0016e6d96751107b7b046e1ffc46 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit You forgot to set the -r flag in the gunzip command. See also manpage of gunzip. On Tue, Jul 7, 2009 at 5:06 PM, Paul Fleurat-Lessard Paul.Fleurat-Lessard= ens-lyon.fr wrote: > > Sent to CCL by: "Paul Fleurat-Lessard" [Paul.Fleurat-Lessard*ens-lyon.fr] > Hi CCL'ers, > > This is not strictly speaking Computational, but it just happens that a > student of mine has archived his files using: > > gzip -cr Dir1 >> Dir1.tar.gz > > According to him, it should be possible to get all files back to a > directory by using: > > gunzip -c Dir1.tar.gz > Dir1 > > but this does not work. If you gunzip the Dir1.tar.gz file, you only get > one file, containing everything and named as the first file of Dir1. > > (Of course, I _had_ told him to use tar -xvzf Dir1.tar.gz Dir1, but he > found the previous scheme on internet.) > > I looked into the Dir1.tar.gz file with hexdump, and there are all the > files together with their name so that it should be possible to extract them > separately. Has anyboddy already faced this ? > > Thanks in advance, > Paul.> > > --0016e6d96751107b7b046e1ffc46 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
You forgot to set the -r flag in the gunzip command. See also manpage o= f gunzip.


On Tue, Jul 7, 2009 at 5:06= PM, Paul Fleurat-Lessard Paul.Fleurat-Lessard=3Dens-lyon.fr <owner-chemistry,+,ccl.net> wrote:

Sent to CCL by: "Paul =C2=A0Fleurat-Lessard" [Paul.Fleurat-Lessar= d*ens-lyon.fr]
Hi CCL'ers,

This is not strictly speaking Computational, but it just happens that a stu= dent of mine has archived his files using:

gzip -cr Dir1 >> Dir1.tar.gz

According to him, it should be possible to get all files back to a director= y by using:

gunzip -c Dir1.tar.gz > Dir1

but this does not work. If you gunzip the Dir1.tar.gz file, you only get on= e file, containing everything and named as the first file of Dir1.

(Of course, I _had_ told him to use tar -xvzf Dir1.tar.gz Dir1, but he foun= d the previous scheme on internet.)

I looked into the Dir1.tar.gz file with hexdump, and there are all the file= s together with their name so that it should be possible to extract them se= parately. Has anyboddy already faced this ?

Thanks in advance,
Paul.



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--0016e6d96751107b7b046e1ffc46-- From owner-chemistry@ccl.net Tue Jul 7 15:22:01 2009 From: "Cristian V. Diaconu cvdiaconu ~~ rice.edu" To: CCL Subject: CCL: Gunzipping a Directory Message-Id: <-39705-090707134511-28490-HOZTfjQFDkfyfjrFAZf/CA(a)server.ccl.net> X-Original-From: "Cristian V. Diaconu" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Jul 2009 12:06:25 -0500 MIME-Version: 1.0 Sent to CCL by: "Cristian V. Diaconu" [cvdiaconu*rice.edu] AFAIK, I'm afraid you cannot extract the files to their original names and locations. Here's an excerpt from gzip manpage: If you wish to create a single archive file with multiple members so that members can later be extracted independently, use an archiver such as tar or zip. GNU tar supports the -z option to invoke gzip transparently. gzip is designed as a complement to tar, not as a replacement. Chris Paul Fleurat-Lessard Paul.Fleurat-Lessard=ens-lyon.fr wrote: > Sent to CCL by: "Paul Fleurat-Lessard" [Paul.Fleurat-Lessard*ens-lyon.fr] > Hi CCL'ers, > > This is not strictly speaking Computational, but it just happens that a student of mine has archived his files using: > > gzip -cr Dir1 >> Dir1.tar.gz > > According to him, it should be possible to get all files back to a directory by using: > > gunzip -c Dir1.tar.gz > Dir1 > > but this does not work. If you gunzip the Dir1.tar.gz file, you only get one file, containing everything and named as the first file of Dir1. > > (Of course, I _had_ told him to use tar -xvzf Dir1.tar.gz Dir1, but he found the previous scheme on internet.) > > I looked into the Dir1.tar.gz file with hexdump, and there are all the files together with their name so that it should be possible to extract them separately. Has anyboddy already faced this ? > > Thanks in advance, > Paul.> > > > -- Cristian V. Diaconu Postdoctoral Research Associate Department of Chemistry - MS60 Rice University PO Box 1892 Houston, TX 77251-1892 Phone: 713-348-3734 Email: cvdiaconu]^[rice.edu From owner-chemistry@ccl.net Tue Jul 7 16:01:01 2009 From: "=?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= jgcj**fct.unl.pt" To: CCL Subject: CCL: Hydrophobicity Message-Id: <-39706-090707120726-19589-ee9Z4tw7a2KL1DO1P/sxVQ*server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= Content-Type: multipart/alternative; boundary=001636c5bd8ce00594046e1f592c Date: Tue, 7 Jul 2009 16:33:57 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= [jgcj^fct.unl.pt] --001636c5bd8ce00594046e1f592c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable you can try http://www.vcclab.org/ gon=E7alo --=20 Gon=E7alo Justino, Ph.D. ---------------------------------------------------- [Computational & Radical BioChemistry] Requimte/CQFB - Department of Chemistry Faculty of Sciences and Technology New University of Lisbon 2829-516 Caparica Portugal Phone: (+351) 212 948 300 ext. 10971 Fax: (+351) 212 948 550 ---------------------------------------------------- All saints have a past, all sinners have a future. 2009/7/7 Tomoko Niwa tmk.niwa_-_gmail.com > Dear Babak > > Please check the following papers: > Tomoko Sotomatsu-Niwa, Akio Ogino, Evaluation of the hydrophobic > parameters of the amino acid side chains of peptides and their > application in QSAR and conformational studies, THEOCHEM (1997), > 392, 43-54. > > Reprints are available on request. > > Hope this helps, > > Tomoko > > =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D > Tomoko Niwa, Ph.D. > Research Lab. Nippon Shinyaku Co., Ltd. > Nishiohji Hachijo Minami-ku Kyoto, 601 Japan > tel 075-321-9047, fax 075-321-9038 > t.niwa at.at nippon-shinyaku.co.jp > =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D > > > > > > 2009/7/7 Babak Khalili khalili.babak:-:gmail.com < > owner-chemistry-*-ccl.net> > >> Dear al >> How can I calculate the hydrophobicity of a peptide? >> >> Thank you for your earliest attention >> Babak khalili Haddad >> > > --001636c5bd8ce00594046e1f592c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable you can try http://www.vcclab.org/
gon=E7alo

--
Gon=E7alo Justino, Ph.D.
---= -------------------------------------------------
[Computational & R= adical BioChemistry]
Requimte/CQFB - Department of Chemistry
Faculty of Sciences and Technolo= gy
New University of Lisbon
2829-516 Caparica
Portugal
Phone: (= +351) 212 948 300 ext. 10971
Fax: (+351) 212 948 550
----------------= ------------------------------------
All saints have a past, all sinners have a future.


2009/7/7 Tomoko Niwa tmk.niwa_-_gmail.com <owner-chemistry~~ccl.net><= br>
Dear Babak
=A0
Please check the following papers:
Tomoko Sotomatsu-Niwa, Akio Ogin= o, Evaluation of the hydrophobic
parameters of the amino acid side chain= s of peptides and their
application in QSAR and conformational studies, = THEOCHEM (1997),
392, 43-54.
=A0
Reprints are available on request.
=A0
Hope this helps,
=A0
Tomoko
=A0
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D
Tomoko Niwa, Ph.D.
Research Lab. Nippon Shinyaku Co.,= Ltd.
Nishiohji Hachijo Minami-ku Kyoto, 601 Japan
tel 075-321-9047, = fax 075-321-9038
t.niwa at.at= nippon-shin= yaku.co.jp
=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D= -=3D-=3D




=A0
2009/7/7 Babak Khalili khalili.babak:-:gmail.com <= ;owner-chemi= stry-*-ccl.net>
Dear al
How ca= n I calculate the hydrophobicity of a peptide?

Thank you for your ea= rliest attention
Babak khalili Haddad


--001636c5bd8ce00594046e1f592c-- From owner-chemistry@ccl.net Tue Jul 7 16:32:00 2009 From: "Ted Cabeen cabeen-$-chem.ucsb.edu" To: CCL Subject: CCL: Gunzipping a Directory Message-Id: <-39707-090707154029-14057-DkToLcB/I+VVYZFo9dqjsA]=[server.ccl.net> X-Original-From: Ted Cabeen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Jul 2009 11:45:12 -0700 MIME-Version: 1.0 Sent to CCL by: Ted Cabeen [cabeen]-[chem.ucsb.edu] I think you're pretty much out of luck for an easy solution. What that command did was the equivalent of concatenating all of the files in Dir1 together, then compressing the resulting file. Unfortunately, that process just places the files one after the other without any indication when one ends and the next begins. You should be able to pick out the breakpoints between each file by hand, or possibly write a script to find them if each file starts the same way, but I don't know of a program that can do that automatically without knowledge of the file formats in question. --Ted Paul Fleurat-Lessard Paul.Fleurat-Lessard=ens-lyon.fr wrote: > Sent to CCL by: "Paul Fleurat-Lessard" [Paul.Fleurat-Lessard*ens-lyon.fr] > Hi CCL'ers, > > This is not strictly speaking Computational, but it just happens that a student of mine has archived his files using: > > gzip -cr Dir1 >> Dir1.tar.gz > > According to him, it should be possible to get all files back to a directory by using: > > gunzip -c Dir1.tar.gz > Dir1 > > but this does not work. If you gunzip the Dir1.tar.gz file, you only get one file, containing everything and named as the first file of Dir1. > > (Of course, I _had_ told him to use tar -xvzf Dir1.tar.gz Dir1, but he found the previous scheme on internet.) > > I looked into the Dir1.tar.gz file with hexdump, and there are all the files together with their name so that it should be possible to extract them separately. Has anyboddy already faced this ? > > Thanks in advance, > Paul.> > From owner-chemistry@ccl.net Tue Jul 7 18:32:01 2009 From: "Babak Khalili khalili.babak-#-gmail.com" To: CCL Subject: CCL: Hydrophobicity Message-Id: <-39708-090707182927-19762-3NSFZ6+BCRtBysZ7gxY3hw/a\server.ccl.net> X-Original-From: Babak Khalili Content-Type: multipart/alternative; boundary=001636c5b8ef7b03c5046e24b2f6 Date: Wed, 8 Jul 2009 02:26:39 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak::gmail.com] --001636c5b8ef7b03c5046e24b2f6 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Goncalo Thank you. It is helpful. Regards, Babak 2009/7/7 Gon=E7alo C. Justino jgcj**fct.unl.pt > you can try http://www.vcclab.org/ > > gon=E7alo > > -- > Gon=E7alo Justino, Ph.D. > ---------------------------------------------------- > [Computational & Radical BioChemistry] > Requimte/CQFB - Department of Chemistry > Faculty of Sciences and Technology > New University of Lisbon > 2829-516 Caparica > Portugal > Phone: (+351) 212 948 300 ext. 10971 > Fax: (+351) 212 948 550 > ---------------------------------------------------- > All saints have a past, all sinners have a future. > > > 2009/7/7 Tomoko Niwa tmk.niwa_-_gmail.com > > > >> Dear Babak >> >> Please check the following papers: >> Tomoko Sotomatsu-Niwa, Akio Ogino, Evaluation of the hydrophobic >> parameters of the amino acid side chains of peptides and their >> application in QSAR and conformational studies, THEOCHEM (1997), >> 392, 43-54. >> >> Reprints are available on request. >> >> Hope this helps, >> >> Tomoko >> >> =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D >> Tomoko Niwa, Ph.D. >> Research Lab. Nippon Shinyaku Co., Ltd. >> Nishiohji Hachijo Minami-ku Kyoto, 601 Japan >> tel 075-321-9047, fax 075-321-9038 >> t.niwa at.at nippon-shinyaku.co.jp >> =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D >> >> >> >> >> >> 2009/7/7 Babak Khalili khalili.babak:-:gmail.com < >> owner-chemistry-*-ccl.net> >> >>> Dear al >>> How can I calculate the hydrophobicity of a peptide? >>> >>> Thank you for your earliest attention >>> Babak khalili Haddad >>> >> >> > --001636c5b8ef7b03c5046e24b2f6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Goncalo

Thank you. It is helpful.

Regards,
Babak
=
2009/7/7 Gon=E7alo C. Justino jgcj**fct.unl.pt <owner-chemistry%a%ccl.net>
you can try http://www.vcclab.org/<= br>
gon=E7alo

--
Gon=E7alo Justino, Ph.D.
---------= -------------------------------------------
[Computational & Radical= BioChemistry]
Requimte/CQFB - Department of Chemistry
Faculty of Sciences and Technolo= gy
New University of Lisbon
2829-516 Caparica
Portugal
Phone: (= +351) 212 948 300 ext. 10971
Fax: (+351) 212 948 550
----------------= ------------------------------------
All saints have a past, all sinners have a future.


2009/7/7 Tomoko Niwa tmk.niwa_-_gmail.com <owner-chemistry^^^ccl.net>
Dear Babak
=A0
Please check the following papers:
Tomoko Sotomatsu-Niwa, Akio Ogin= o, Evaluation of the hydrophobic
parameters of the amino acid side chain= s of peptides and their
application in QSAR and conformational studies, = THEOCHEM (1997),
392, 43-54.
=A0
Reprints are available on request.
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Hope this helps,
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Tomoko
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=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D
Tomoko Niwa, Ph.D.
Research Lab. Nippon Shinyaku Co.,= Ltd.
Nishiohji Hachijo Minami-ku Kyoto, 601 Japan
tel 075-321-9047, = fax 075-321-9038
t.niwa at.at= nippon-shin= yaku.co.jp
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2009/7/7 Babak Khalili khalili.babak:-:gmail.com <owner-c= hemistry-*-ccl.net>

Dear al
How ca= n I calculate the hydrophobicity of a peptide?

Thank you for your ea= rliest attention
Babak khalili Haddad



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