From owner-chemistry@ccl.net Mon May 26 05:05:00 2008 From: "Michael Shokhen shokhen/a\mail.biu.ac.il" To: CCL Subject: CCL: Software for molecular databank creation Message-Id: <-37033-080526050020-18028-9H+ZykMBpG7DtUHWWywTuw_-_server.ccl.net> X-Original-From: "Michael Shokhen" Date: Mon, 26 May 2008 05:00:15 -0400 Sent to CCL by: "Michael Shokhen" [shokhen#%#mail.biu.ac.il] Dear Colleagues, I want to collect information (molecular structure, biding affinity)about inhibitors from literature and molecular databanks. My purpose is to organize the collected data as input files for the following molecular modeling and drug design. In other words I am looking for MS Windows platform software tool for creation of my own molecular databank that can read/write SD,SDF, XLS files format and then represent these data as a table in MS Excel manner, where every field including molecular structures will be active for editing. I would appreciate if somebody can recommend me a relevant software. Please dont mention the Accelrys Accord for Excel ! Thank you, Michael From owner-chemistry@ccl.net Mon May 26 07:30:00 2008 From: "Arthur computationalboy===gmail.com" To: CCL Subject: CCL: Software for molecular databank creation Message-Id: <-37034-080526072117-25185-Cm8e+CG48w7nrJaEuJP3jg(a)server.ccl.net> X-Original-From: "Arthur" Content-Type: multipart/alternative; boundary="----=_NextPart_08042217253640635620727_002" Date: Tue, 22 Apr 2008 17:25:38 +0800 MIME-Version: 1.0 Sent to CCL by: "Arthur"[computationalboy+*+gmail.com] ------=_NextPart_08042217253640635620727_002 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 SSBqdXN0IHJlY29tbWVuZCBNREwgSVNJUy9CYXNlLCB0aG91Z2ggaXQncyBjb21tZXJpY2lhbGx5 IGF2YWlsYWJsZSENCg0KDQpBcnRodXIsIGNvbXB1dGF0aW9uYWxib3lAZ21haWwuY29tDQoyMDA4 LTA0LTIyIA0KLS0tLS0gUmVjZWl2aW5nIHRoZSBmb2xsb3dpbmcgY29udGVudCAtLS0tLSANCkZy b206IE1pY2hhZWwgU2hva2hlbiBzaG9raGVuL2FcbWFpbC5iaXUuYWMuaWwgDQpSZWNlaXZlcjog V2FuZyxKaWFuIC1pZCM0bjMtIA0KVGltZTogMjAwOC0wNS0yNiwgMTc6MDA6MTUNClN1YmplY3Q6 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X-Original-From: andras.borosy-*-givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 00447B72C1257455_=" Date: Mon, 26 May 2008 14:27:58 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy]_[givaudan.com This is a multipart message in MIME format. --=_alternative 00447B72C1257455_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable I do not suggest ISIS Base, because it is very expensive. Better choices: 1. MOE (it is the best, but it is more expensive, because it offers much=20 more then a db manager): http://www.chemcomp.com 2. Chemaxon: http://www.chemaxon.com/ 3. Chemfinder: http://chemfinder.cambridgesoft.com/ Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Arthur computationalboy=3D=3D=3Dgmail.com" =20 Sent by: owner-chemistry%x%ccl.net 22.04.2008 11:25 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Software for molecular databank creation I just recommend MDL ISIS/Base, though it's commericially available! =20 =20 Arthur, computationalboy%x%gmail.com 2008-04-22=20 ----- Receiving the following content -----=20 > From: Michael Shokhen shokhen/a\mail.biu.ac.il=20 Receiver: Wang,Jian =20 Time: 2008-05-26, 17:00:15 Subject: CCL: Software for molecular databank creation Sent to CCL by: "Michael Shokhen" [shokhen#%#mail.biu.ac.il] Dear Colleagues, I want to collect information (molecular structure, biding affinity)about=20 inhibitors from literature and molecular databanks. My purpose is to=20 organize the collected data as input files for the following molecular=20 modeling and drug design. In other words I am looking for MS Windows=20 platform software tool for creation of my own molecular databank that can=20 read/write SD,SDF, XLS files format and then represent these data as a=20 table in MS Excel manner, where every field including molecular structures = will be active for editing. I would appreciate if somebody can recommend me a relevant software. Please dont mention the Accelrys Accord for Excel !=20 Thank you, Michael -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 00447B72C1257455_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
I do not suggest ISIS Base, because it is very expensive.

Better choices:

1. MOE (it is the best, but it is mo= re expensive, because it offers  much more then a db manager): http://www= .chemcomp.com
2. Chemaxon: http://www.chemaxon.com= /
3. Chemfinder: http://chemfinder.cam= bridgesoft.com/

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com



"Arthur computat= ionalboy=3D=3D=3Dgmail.com" <owner-chemistry%x%ccl.net>
Sent by: owner-chemistry%x%ccl.net

22.04.2008 11:25
Please respond to
"CCL Subscribers" <chemistry%x%ccl.net>
To
"Borosy, Andras " <andras.borosy%x%givaudan.com>
cc
Subject
CCL: Software for molecular databank creation





I just recommend MDL ISIS/Base, thou= gh it's commericially available!
 
 
Arthur, = computationalboy%x%gmail.com
2008-04-22
----- Receiving the following content -----
From: = Michael Shokhen shokhen/a\mail.biu.ac.il
Receiver: Wang,Jian
Time: 2008-05-26, 17:00:15
Subject: CCL: Software for mo= lecular databank creation

Sent to CCL by: "Michael Shokhe= n" [shokhen#%#mail.biu.ac.il]
Dear Colleagues,

I want to collect information (molecular structure, biding affinity)about inhibitors from literature and molecular databanks. My purpose is to organi= ze the collected data as input files for the following molecular modeling and drug design. In other words I am looking for MS Windows platform softwa= re tool for creation of my own molecular databank that can read/write SD,SDF, XLS files format and then represent these data as a table in MS Excel manne= r, where every field including molecular structures will be active for editing= .
I would appreciate if somebody can recommend me a relevant software.
Please dont mention the Accelrys Accord for Excel !

Thank you,
Michael



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--=_alternative 00447B72C1257455_=-- From owner-chemistry@ccl.net Mon May 26 10:52:00 2008 From: "Mike Devereux Michael.Devereux*unibas.ch" To: CCL Subject: CCL:G: Gaussian Field Keyword Sign Convention Message-Id: <-37036-080526040950-12336-lE52QOoe25jGYsmWvCtSBQ ~~ server.ccl.net> X-Original-From: "Mike Devereux" Date: Mon, 26 May 2008 04:09:46 -0400 Sent to CCL by: "Mike Devereux" [Michael.Devereux/./unibas.ch] Dear CCLers, does anyone know the sign convention for the dipole electric field available via the 'FIELD' keyword in Gaussian 03? I normally think of an electric field as pointing from positive charge to negative charge, but I would say a dipole points from negative charge to positive charge, so which way does the dipole field point? Many thanks! Mike Devereux From owner-chemistry@ccl.net Mon May 26 12:11:01 2008 From: "Forlani Roberto roberto.forlani:-:nikemresearch.com" To: CCL Subject: CCL: Software for molecular databank creation Message-Id: <-37037-080526120438-28604-EUHSIZJ0NH8yFYOKuZpMkA||server.ccl.net> X-Original-From: "Forlani Roberto" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 26 May 2008 17:31:43 +0200 MIME-Version: 1.0 Sent to CCL by: "Forlani Roberto" [roberto.forlani{}nikemresearch.com] > ----- Receiving the following content -----=20 > > From: Michael Shokhen shokhen/a\mail.biu.ac.il=20 > Receiver: Wang,Jian =20 > Time: 2008-05-26, 17:00:15 > Subject: CCL: Software for molecular databank creation >=20 > Sent to CCL by: "Michael Shokhen" [shokhen#%#mail.biu.ac.il] > Dear Colleagues, >=20 > I want to collect information (molecular structure, biding=20 > affinity)about=20 > inhibitors from literature and molecular databanks. My purpose is to=20 > organize the collected data as input files for the following=20 > molecular=20 > modeling and drug design. In other words I am looking for MS Windows=20 > platform software tool for creation of my own molecular=20 > databank that can=20 > read/write SD,SDF, XLS files format and then represent these=20 > data as a=20 > table in MS Excel manner, where every field including=20 > molecular structures=20 > will be active for editing. > I would appreciate if somebody can recommend me a relevant software. > Please dont mention the Accelrys Accord for Excel !=20 >=20 > Thank you, > Michael >=20 Hi Michael, check if sMol Explorer can fit your requirements. http://www.biotec.or.th/isl/sMOL/Features.asp HTH, roberto =20 From owner-chemistry@ccl.net Mon May 26 22:01:01 2008 From: "Arthur computationalboy|*|gmail.com" To: CCL Subject: CCL: software for plotting hydrophobic interactions Message-Id: <-37038-080526211559-1772-eDAy5arUVRUdMo0s1jdFiw]_[server.ccl.net> X-Original-From: Arthur Content-Type: multipart/alternative; boundary="----=_Part_8698_20844372.1211847700447" Date: Tue, 27 May 2008 08:21:40 +0800 MIME-Version: 1.0 Sent to CCL by: Arthur [computationalboy__gmail.com] ------=_Part_8698_20844372.1211847700447 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all: Can anyone recommend software for displaying hydrophobic interactions? I know ligplot and ligandexplorer can do this. However, I need some others. Thanks in advance! -- Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China Tel : +86 24 23986419 Fax: +86 24 23995043 E-Mail: wjmed(at)126.com ; computationalboy(at)gmail.com ------=_Part_8698_20844372.1211847700447 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all:
Can anyone recommend software for displaying hydrophobic interactions?
I know ligplot and ligandexplorer can do this. However, I need some others.
Thanks in advance!

--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail: wjmed(at)126.com ;
computationalboy(at)gmail.com ------=_Part_8698_20844372.1211847700447-- From owner-chemistry@ccl.net Mon May 26 23:42:01 2008 From: "Carlos F. Lagos carlos~!~cbuc.cl" To: CCL Subject: CCL: Weak acid/Weak base Message-Id: <-37039-080526123827-9521-1GTRAUkkOwXQryg0rSty+Q..server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0014_01C8BF27.17ADB930" Date: Mon, 26 May 2008 11:53:20 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos(-)cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C8BF27.17ADB930 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Try ADME/Tox web at Pharma-Algorithms http://www.pharma-algorithms.com/webboxes/ See your molecule at Ionization or Protein Binding tools using SMILES QF Carlos Lagos A. Centre for Bioinformatics CB, Faculty of Biological Sciences Medicinal Chemistry Laboratory, Faculty of Chemistry P. Universidad Catolica de Chile Portugal # 49 - ZIP 6513492 Santiago - Chile Phone: + 56 2 6862269; http://www.cbuc.cl _____ De: owner-chemistry(_)ccl.net [mailto:owner-chemistry(_)ccl.net] Enviado el: viernes, 23 de mayo de 2008 18:56 Para: Lagos, Carlos F Asunto: CCL: Weak acid/Weak base Hi all, I was wondering if someone could point me in the direction of some software that can calculate if a molecule is a weak acid or a weak base please? Thanks Iain ------=_NextPart_000_0014_01C8BF27.17ADB930 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Try ADME/Tox = web at Pharma-Algorithms

http://www.pharma-alg= orithms.com/webboxes/

See your = molecule at Ionization or Protein Binding tools using SMILES

QF Carlos Lagos A.
Centre for Bioinformatics CB, Faculty of Biological Sciences
Medicinal Chemistry Laboratory, Faculty of Chemistry
P. Universidad Catolica de Chile
Portugal # 49 – ZIP 6513492
Santiago – Chile
Phone: + 56 2 6862269; http://www.cbuc.cl  

De: owner-chemistry(_)ccl.net [mailto:owner-chemistry(_)ccl.net]
Enviado el: viernes, 23 = de mayo de 2008 18:56
Para: Lagos, Carlos F =
Asunto: CCL: Weak = acid/Weak base

 

Hi all,

I was wondering if someone could point me in the direction of some = software that can calculate if a molecule is a weak acid or a weak base = please?

Thanks

Iain

------=_NextPart_000_0014_01C8BF27.17ADB930--