From chemistry-request@ccl.net Wed Sep 1 13:37:11 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i81Ib9nI012264 for ; Wed, 1 Sep 2004 13:37:09 -0500 Received: from localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 1E64547F53; Wed, 1 Sep 2004 14:44:47 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 32570-08; Wed, 1 Sep 2004 14:44:41 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 271C447FA3; Wed, 1 Sep 2004 14:42:34 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Wed, 1 Sep 2004 14:42:33 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: predict 3D structure from sequence Date: Wed, 1 Sep 2004 14:42:33 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA000492E501/at/srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: predict 3D structure from sequence Thread-Index: AcSQUEkVCiPLLNbDQwWKPj0v5Hqa2wAAtHUw From: "Shobe, David" To: "J. Zheng" , X-OriginalArrivalTime: 01 Sep 2004 18:42:33.0962 (UTC) FILETIME=[71D3FCA0:01C49053] X-Spam-Status: No, hits=4.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i81IbBnI012275 I understand some progress has been made in the past decade, but this is still an unsolved problem, isn't it? --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On Behalf Of J. Zheng Sent: Wednesday, September 01, 2004 12:57 PM To: chemistry/at/ccl.net Subject: CCL:predict 3D structure from sequence hi, folks: Do you know any software can predict 3D structure of protein according the sequence of amino acid? Jie ----------------------------------------------- | JIE ZHENG | | Graduate Student | | Department of Chemical Engineering | | University of Washington | | Seattle, WA 98105, USA | ----------------------------------------------- | Tel: (206) 529-1373 (h) | | (206) 616-6510 (o) | | Email: jzheng73/at/u.washington.edu | ----------------------------------------------- -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY/at/ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Wed Sep 1 16:06:35 2004 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i81L6WnI024257 for ; Wed, 1 Sep 2004 16:06:33 -0500 Received: from caracas-2111.adsl.interware.hu ([213.178.108.63] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.34 #1 (Debian)) id 1C2cSE-0002KJ-U4; Wed, 01 Sep 2004 23:15:43 +0200 Message-ID: <000d01c49071$9dde1ce0$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: "Raju Vishwanathan" , References: <000401c48ff0$4a813040$6666a8c0/at/agi.com> Subject: Re: CCL: Problem encountered in Marvin Editor Date: Wed, 1 Sep 2004 23:18:17 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I do not understand exactly the problem. The coordinates of a 2D molfile, originating for example from an ISIS sketch, hasn't too much to do with the 3D reality, they are usually kind of arbitrary coordinates. Anyway, you should contact with ChemAxon, the producer of Marvin. http://www.chemaxon.com/products.html Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu ----- Original Message ----- From: "Raju Vishwanathan" To: Sent: Wednesday, September 01, 2004 7:52 AM Subject: CCL:Problem encountered in Marvin Editor > Hi CCL memebers, > > I am working on 2D MDL Mol files. > My existing 2D Mol files were opened in Marvin Editor and again saved it as > (.MOL) file. Just curious enough to check the Mol structure file. > And to my surprise the Co-ordinates for the same structure has changed. > (Though the structure is the same). I repeated this for my all structures, > co-ordinates have changed. > > Has anybody tried this and already reported. Please let me know. > > I repeated this with all my 3D MDL Mol files. The same co-ordinate problem > is repeating! This has serious implications in 3D descriptors??? > The 3D descriptor values no longer remain the same for the same structure. > > I would be glad if you could give your comments and feedback to solve this > problem!!!!!!! > > > Thanking you, > Warm Regards, > Raju Vishwanathan > Sr. Consultant > SysArris Software > # 120 A, Elephant Rock Road, > III Block, Jayanagar,( Opp to HSBC ATM ). > Bangalore-560011 > India. > Tel. No. 91-80-26654965,26655052,26642690, > Fax No. 91-80-26650374 > <> > The information in this message is conf dential and may be legally > privileged. It is intended solely for the addressee. Access to this message > by anyone else is unauthorised. If you are not the intended recipient, any > disclosure, copying, or distribution of the message, or any action or > omission taken by you in reliance on it, is prohibited and may be unlawful. > Please immediately contact the sender if you have received this message in > error.Thank you. > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY/at/ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Sep 2 02:58:18 2004 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i827wF1J027899 for ; Thu, 2 Sep 2004 02:58:16 -0500 Received: from [10.0.0.149] (148.123-182-adsl-pool.axelero.hu [81.182.123.148]) by chemaxon.hu (8.12.8/8.12.8) with ESMTP id i8287TOm006092; Thu, 2 Sep 2004 10:07:29 +0200 Message-ID: <4136D4A3.8030205{at}chemaxon.com> Date: Thu, 02 Sep 2004 10:06:59 +0200 From: Alex Allardyce Reply-To: aa{at}chemaxon.com User-Agent: Mozilla Thunderbird 0.7 (Windows/20040616) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry{at}ccl.net Subject: RE. Problem encountered in Marvin Editor Content-Type: multipart/alternative; boundary="------------060100030001040806030002" X-Spam-Status: No, hits=4.2 required=7.5 tests=EXCUSE_16,HTML_MESSAGE, HTML_TITLE_EMPTY,MY_DSL,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------060100030001040806030002 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi Raju, I have forwarded this message to our Technical Support Forum where is has been/is being discussed here . Cheers Alex -- Alex Allardyce Communications Director Chemaxon Ltd Maramaros kvz 3/a Budapest, 1037 Hungary Tel.: +361 4532658 Fax.: +361 4532659 e-mail: aa{at}chemaxon.com Hi CCL memebers, I am working on 2D MDL Mol files. My existing 2D Mol files were opened in Marvin Editor and again saved it as (.MOL) file. Just curious enough to check the Mol structure file. And to my surprise the Co-ordinates for the same structure has changed. (Though the structure is the same). I repeated this for my all structures, co-ordinates have changed. Has anybody tried this and already reported. Please let me know. I repeated this with all my 3D MDL Mol files. The same co-ordinate problem is repeating! This has serious implications in 3D descriptors??? The 3D descriptor values no longer remain the same for the same structure. I would be glad if you could give your comments and feedback to solve this problem!!!!!!! Thanking you, Warm Regards, Raju Vishwanathan Sr. Consultant SysArris Software # 120 A, Elephant Rock Road, III Block, Jayanagar,( Opp to HSBC ATM ). Bangalore-560011 India. Tel. No. 91-80-26654965,26655052,26642690, Fax No. 91-80-26650374 <> The information in this message is conf dential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, or distribution of the message, or any action or omission taken by you in reliance on it, is prohibited and may be unlawful. Please immediately contact the sender if you have received this message in error.Thank you. --------------060100030001040806030002 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 
Hi Raju,

I have forwarded this message to our Technical Support Forum where is has been/is being discussed here.

Cheers

Alex

-- 
Alex Allardyce
Communications Director

Chemaxon Ltd
Máramaros köz 3/a
Budapest, 1037 Hungary
Tel.: +361 4532658
Fax.: +361 4532659

e-mail: aa{at}chemaxon.com

Hi CCL memebers,

I am working on 2D MDL Mol files.
My existing 2D Mol files were opened in Marvin Editor and again saved it as
(.MOL) file. Just curious enough to check the Mol structure file.
And to my surprise the Co-ordinates for the same structure has changed.
(Though the structure is the same). I repeated this for my all structures,
co-ordinates have changed.

Has anybody tried this and already reported. Please let me know.

I repeated this with all my 3D MDL Mol files. The same co-ordinate problem
is repeating! This has serious implications in 3D descriptors???
The 3D descriptor values no longer remain the same for the same structure.

I would be glad if you could give your comments and feedback to solve this
problem!!!!!!!


Thanking you,
Warm Regards,
Raju Vishwanathan
Sr. Consultant
SysArris Software
# 120 A, Elephant Rock Road,
III Block, Jayanagar,( Opp to HSBC ATM ).
Bangalore-560011
India.
Tel. No. 91-80-26654965,26655052,26642690,
Fax No. 91-80-26650374
<<http://www.sysarris.com/>>
The information in this message is conf dential and may be legally
privileged. It is intended solely for the addressee. Access to this message
by anyone else is unauthorised. If you are not the intended recipient, any
disclosure, copying, or distribution of the message, or any action or
omission taken by you in reliance on it, is prohibited and may be unlawful.
Please immediately contact the sender if you have received this message in
error.Thank you.




--------------060100030001040806030002--


From chemistry-request@ccl.net Thu Sep  2 10:11:21 2004
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Date: Thu, 02 Sep 2004 17:06:38 +0200
To: chemistry!at!ccl.net
From: Barry Hardy 
Subject: InterNanotech Community launch
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The InterNanotech Community of Practice in computational and experimental 
nanotechnology launches next week at the Pacific Rim Conference in 
Nanoscience, Broome, Australia.  The conference is chaired by Professor 
Nick Quirke, Imperial College London, includes contributions from leading 
researchers in the Pacific Region, in addition to invited speakers from 
Europe and the USA, and contains a significant amount of advanced 
computational chemistry applied to nanotech research problems.

All lectures including slides and audio from the conference will be 
available through the Web site located at http://nanotech.colayer.net/.

This community project is an international, interdisciplinary community for 
scientists working in research areas of relevance to nanoscience and 
nanotechnology.

The activities of the community support the rapid exchange of new research 
results and discussion in experimental and computational nanoscience. 
Members can attend regular Virtual Seminar sessions to keep up with 
research news and results from leading experts in the field.

Oversight, advice and guidance of the scientific program is provided by a 
Scientific Advisory Board, chaired by Prof. Nick Quirke of Imperial College 
London.

Running November 2004: Modelling of Membranes and Ion Channels, chaired by 
Richard Pastor, FDA CBER, USA

Running in 2005: International Conference in Experimental & Computational 
Nanoscience, 2005

Topics: Nanofluidics, nanobiology, nanofabrication, nanoparticles, 
computational nanoscience, nanomaterials, nanodevices, nanoelectronics, 
molecular manufacturing, activated carbon and zeolite design, 
self-assembly, health, safety, environmental and medical applications.

Conference sessions will be held monthly in Spring and Autumn 2005.

Call for Seminars/Papers: Please submit a short summary proposal for a 
proposed session you would be interested in chairing (ca. 500 words) or for 
a talk you would wish to present (ca. 300 words) to 
nanotech!at!douglasconnect.com by 31 October 2004.

All papers will be considered for publication in Molecular Simulation and 
the forthcoming Journal of Experimental Nanoscience (first issue, January 
2006).

best regards
Barry Hardy



Barry Hardy, PhD
Douglas Connect, Switzerland
www.douglasconnect.com
+41 61 851 0170 (office)
+41 79 755 2340 (mobile)
Email: barry.hardy!at!tiscalinet.ch

--=====================_34993221==_.ALT
Content-Type: text/html; charset="us-ascii"




The InterNanotech Community of Practice in computational and experimental
nanotechnology launches next week at the Pacific Rim Conference in
Nanoscience, Broome, Australia.  The conference is chaired by
Professor Nick Quirke, Imperial College London, includes contributions
> from leading researchers in the Pacific Region, in addition to invited
speakers from Europe and the USA, and contains a significant amount of
advanced computational chemistry applied to nanotech research
problems.



All lectures including slides and audio from the conference will be
available through the Web site located at
http://nanotech.colayer.net/.



This community project is an international, interdisciplinary community
for scientists working in research areas of relevance to nanoscience and
nanotechnology.



The activities of the community support the rapid exchange of new
research results and discussion in experimental and computational
nanoscience. Members can attend regular Virtual Seminar sessions to keep
up with research news and results from leading experts in the 
field.



Oversight, advice and guidance of the scientific program is provided by a
Scientific Advisory Board, chaired by Prof. Nick Quirke of Imperial
College London.



Running November 2004: Modelling of Membranes and Ion Channels,
chaired by Richard Pastor, FDA CBER, USA



Running in 2005: International Conference in Experimental &
Computational Nanoscience, 2005



Topics: Nanofluidics, nanobiology, nanofabrication, nanoparticles,
computational nanoscience, nanomaterials, nanodevices, nanoelectronics,
molecular manufacturing, activated carbon and zeolite design,
self-assembly, health, safety, environmental and medical
applications.



Conference sessions will be held monthly in Spring and Autumn 2005. 




Call for Seminars/Papers: Please submit a short summary proposal for a
proposed session you would be interested in chairing (ca. 500 words) or
for a talk you would wish to present (ca. 300 words) to
nanotech!at!douglasconnect.com by 31 October 2004.



All papers will be considered for publication in Molecular
Simulation and the forthcoming Journal of Experimental
Nanoscience (first issue, January 2006). 



best regards

Barry Hardy







Barry Hardy, PhD 

Douglas Connect, Switzerland

www.douglasconnect.com


+41 61 851 0170 (office) 

+41 79 755 2340 (mobile)

Email: barry.hardy!at!tiscalinet.ch 



--=====================_34993221==_.ALT--



From chemistry-request@ccl.net Thu Sep  2 09:03:08 2004
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Date: Thu, 02 Sep 2004 10:12:08 -0400
From: "Lei Wang" 
To: , 
Subject: Re: CCL:predict 3D structure from sequence
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There are two approach, with the 3D structure of a template, or without.
The first one called Camparative Protein Modeling, which requires a 3d
structure of a protein, which has >30% sequence Similarity comparing to
target. It's pretty reliable.  The second approach has lower success
rate..

>>> "Shobe, David"  9/1/2004 2:42:33 PM >>>
I understand some progress has been made in the past decade, but this
is still an unsolved problem, isn't it?

--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.



-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request!at!ccl.net]On

Behalf Of J. Zheng
Sent: Wednesday, September 01, 2004 12:57 PM
To: chemistry!at!ccl.net 
Subject: CCL:predict 3D structure from sequence



hi, folks:

Do you know any software can predict 3D structure of protein according
the
sequence of amino acid?

Jie

-----------------------------------------------
|  JIE ZHENG                          	      |
|  Graduate Student			      |
|  Department of Chemical Engineering	      |
|  University of Washington		      |
|  Seattle, WA 98105, USA   		      |
-----------------------------------------------
|  Tel:  (206) 529-1373 (h)		      |
|        (206) 616-6510 (o)		      |
| Email: jzheng73..at..u.washington.edu	      |
-----------------------------------------------












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From chemistry-request@ccl.net Thu Sep  2 08:37:46 2004
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Date: Thu, 2 Sep 2004 14:47:00 +0100 (BST)
From: =?iso-8859-1?q?Jeff=20C?= 
Subject: Queries: GAMESS-UK and 3D QSAR 
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Dear CCL scientists,

I am a novice who is currently learning GAMESS-UK. Can
someone please tell me what is the silly mistake I am
making when after my calculation is completed, I can t
find the optimised atomic coordinates. I know this
must be trivial to most of you but your input would
really help me tremendously. In addition, can any one
also please kindly tell me what is the most affordable
(yet efficient) 3D QSAR software used in drug design. 


Much appreciated.

Best regards

Jeff   



	
	
		
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Thread-Topic: CCL: octanol-water partition coefficient calculations for peptides/small proteins
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From: "LEDM (Leonardo De Maria)" 
To: 
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Hi out there,

can anyone point my attention to software to calculate the
octanol-water partition coefficient calculations of
peptides/small proteins (10-40 amino acids) besides PLOGP?

It will be appreciated if they use 3D information for that
purpose.

Regards,

Leonardo De Maria, PhD	Novozymes A/S
Research Scientist
Brudelysvej 26			Bygning 1U.S25
Protein Design			2880 Bagsveard
Molecular Biotechnology		Denmark		=09
	+45 44421890 direct
	+45 44980246 fax=09
LeDM..at..novozymes.com 		www.novozymes.com


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CCL: octanol-water partition coefficient calculations for =
peptides/small proteins





Hi out there,




can anyone point my attention to =
software to calculate the


octanol-water partition =
coefficient calculations of


peptides/small proteins (10-40 =
amino acids) besides PLOGP?




It will be appreciated if they =
use 3D information for that


purpose.




Regards,




Leonardo De =
Maria, PhD  Novozymes A/S


Research Scientist


Brudelysvej 26  =
        =
        Bygning 1U.S25


Protein Design  =
        =
        2880 Bagsveard


Molecular Biotechnology =
        Denmark =
        =
        


        =
+45 44421890 =
direct


        =
+45 44980246 =
fax        


LeDM..at..novozymes.com      =
        www.novozymes.com





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