Subject: software for lead optimisation?

From: Monika Rella <bmbmre:at:bmb.leeds.ac.uk>
Date: Fri, 13 Feb 2004 17:23:23 +0000

Hello CCLers!

Can anyone please advise me about free software for lead optimisation? I'm 
thinking about a tool like LUDI or Sybyl's RACHEL module that performs 
"automated combinatorial optimization of lead compounds by systematically 
derivatizing user-defined sites on the ligand". Any suggestions wellcome!

Regards,

Monika
-- 
******************************************************************************************
Monika Rella
PhD Bioinformatics Research Student
School of Biochemistry and Molecular Biology
University of Leeds, LS2 9JT, UK
E-mail: bmbmre:at:bmb.leeds.ac.uk
Tel: +44 (0) 113 343 4447
*****************************************************************************************

Return-Path: <[email-masked]>
Message-ID: <1077565653.403a58d57a2ee-.at.-www.whitman.edu>
Date: Mon, 23 Feb 2004 11:47:33 -0800
From: chishotr-.at.-whitman.edu
To: chemistry-.at.-ccl.net
Subject: Question on using AutoDock 3.0

I am attempting to use AutoDock 3.0 free of charge from Scripps in order to do 
molecular docking and modeling and am having a bit of trouble.  I am using a 
MacOS X platform, and have downloaded and located the appropriate executables, 
but am unable to get them to run.  When I click on the "AutoDock" executable, 
it brings up a Unix terminal with the following message:

Last login: Mon Feb 23 11:39:35 on ttyp1
/Users/biology/Desktop/autodock3; exit
Welcome to Darwin!
SCI-317-03:~ biology$ /Users/biology/Desktop/autodock3; exit
Segmentation fault
logout
[Process completed]

Does anyone have any information that could help me with this problem?  My Unix 
knowledge is fairly limited, so any relevant information would be much 
appreciated.  Thank you very much for your help.

Tyler Chisholm
Whitman College
Walla Walla, WA 99362

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To: chemistry~at~ccl.net
Subject: 04.06.04 Accelrys Catalyst User Group Meeting, Tarrytown, NY
From: Samuel Toba <stoba~at~accelrys.com>
Date: Tue, 17 Feb 2004 12:36:28 -0800

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5th Annual U.S. Catalyst User Group Meeting

June 4th, 2004

Emisphere Technologies, Inc
Tarrytown, NY

Registration deadline May 28, 2004

We are pleased to announce that this year?s US Catalyst User Group Meeting =

(UGM) will be held on Friday, June 4th, 2004.  The meeting will be hosted=20
by Dr. Isabel Gomez-Orellana of Emisphere Technologies, Inc., and will be=20
held at the Emisphere?s facility located in Tarrytown, N.Y., just 40=20
minutes north of Manhattan.  Registration and agenda information for this=20
event have been posted at the URL below:=20

http://www.accelrys.com/usergroups/catalyst/2004/us/

The website will be updated as more speakers and topics are finalized.=20
Please register for this event as soon as possible, before the=20
registration deadline of  Friday, May 28, 2004.   We also encourage you to =

consider presenting some of your work at the meeting. Abstract submission=20
can be included in the on-line registration. Your participation will=20
ensure a successful Catalyst UGM.=20

Tarrytown is easily accessible from many major and local airports=20
including LaGuardia Airport, JFK Airport, Newark Airport, and Westchester=20
County Airport. Emisphere?s facility is closest to Westchester County=20
Airport (approximately 20 minutes) and about an hour from all other=20
airports.  There are a number of hotels available near the Emisphere=20
Technologies site. Some of these are listed on the website.

An important aspect of this meeting will be the opportunity to learn and=20
discuss issues such as: (1) Applications of Catalyst and pharmacophores in =

drug-discovery and chemical-sciences by users, (2) Securing intellectual=20
property for pharmacophore models and chemical space, (3) New and future=20
technologies within the Catalyst release, (4) Catalyst platforms on Linux, =

SGI and IBM, and (5) Users input into future enhancements to the Catalyst=20
program.  This is a great opportunity to meet with other Catalyst users=20
and some of the Catalyst developers and discuss the future direction of=20
this important software tool.=20

We look forward to seeing many of you in Tarrytown, NY on June 4, 2004.=20

Best Regards,=20

Isabel Gomez-Orellana, Ph.D. (Emisphere Technologies, Inc.)
Samuel Toba, Ph.D.  (Accelrys)

------
Samuel Toba, Ph.D.
Product Specialist, Catalyst
Rational Drug Design
Accelrys, Inc.
9685 Scranton Road
San Diego, CA 92121-3752
Direct: 858-799-5567
Fax: 858-799-5777
Email: stoba~at~accelrys.com

Catalyst products:
http://www.accelrys.com/catalyst/

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<br><font size=3D2 face=3D"sans-serif">Hi Jan...</font>
<br>
<br><font size=3D2 face=3D"sans-serif">Could you please post this in CCL? T=
hank
you...</font>
<br>
<br><font size=3D2 face=3D"sans-serif">Cheers,</font>
<br>
<br><font size=3D2 face=3D"sans-serif">-Samuel</font>
<br>
<br>
<div align=3Dcenter>
<br><font size=3D4 face=3D"Times New Roman"><b>5th Annual U.S. Catalyst User
Group Meeting</b></font>
<br>
<br><font size=3D3 face=3D"Times New Roman"><b>June 4th, 2004</b></font>
<br>
<br><font size=3D3 face=3D"Times New Roman"><b>Emisphere Technologies, Inc<=
/b></font>
<br><font size=3D3 face=3D"Times New Roman"><b>Tarrytown, NY</b></font>
<br>
<br><font size=3D3 face=3D"Times New Roman"><b>Registration deadline May 28,
2004</b></font></div>
<br>
<br>
<br><font size=3D3 face=3D"Times New Roman">We are pleased to announce that
this year&#8217;s US Catalyst User Group Meeting (UGM) will be held on Frid=
ay,
June 4th, 2004. &nbsp;The meeting will be hosted by Dr. Isabel Gomez-Orella=
na
of Emisphere Technologies, Inc., and will be held at the Emisphere&#8217;s =
facility
located in Tarrytown, N.Y., just 40 minutes north of Manhattan. &nbsp;Regis=
tration
and agenda information for this event have been posted at the URL below:
</font>
<br>
<br><font size=3D3 color=3Dblue face=3D"Times New Roman"><u>http://www.acce=
lrys.com/usergroups/catalyst/2004/us/</u></font>
<br>
<br><font size=3D3 face=3D"Times New Roman">The website will be updated as
more speakers and topics are finalized. Please register for this event
as soon as possible, before the registration deadline of <u>&nbsp;<b>Friday,
May 28, 2004</u></b><u>.</u> &nbsp; We also encourage you to consider prese=
nting
some of your work at the meeting. Abstract submission can be included in
the on-line registration. Your participation will ensure a successful Catal=
yst
UGM. </font>
<br>
<br><font size=3D3 face=3D"Times New Roman">Tarrytown is easily accessible
> from many major and local airports including LaGuardia Airport, JFK Airport,
Newark Airport, and Westchester County Airport. Emisphere&#8217;s facility =
is
closest to Westchester County Airport (approximately 20 minutes) and about
an hour from all other airports. &nbsp;There are a number of hotels availab=
le
near the Emisphere Technologies site. Some of these are listed on the websi=
te.</font>
<br>
<br><font size=3D3 face=3D"Times New Roman">An important aspect of this mee=
ting
will be the opportunity to learn and discuss issues such as: (1) Applicatio=
ns
of Catalyst and pharmacophores in drug-discovery and chemical-sciences
by users, (2) Securing intellectual property for pharmacophore models and
chemical space, (3) New and future technologies within the Catalyst release,
(4) Catalyst platforms on Linux, SGI and IBM, and (5) Users input into
future enhancements to the Catalyst program. &nbsp;This is a great opportun=
ity
to meet with other Catalyst users and some of the Catalyst developers and
discuss the future direction of this important software tool. </font>
<br>
<br><font size=3D3 face=3D"Times New Roman">We look forward to seeing many
of you in Tarrytown, NY on June 4, 2004. </font>
<br>
<br><font size=3D3 face=3D"Times New Roman">Best Regards, </font>
<br>
<br><font size=3D3 face=3D"Times New Roman">Isabel Gomez-Orellana, Ph.D. (E=
misphere
Technologies, Inc.)</font>
<br><font size=3D3 face=3D"Times New Roman">Samuel Toba, Ph.D. &nbsp;(Accel=
rys)</font>
<br>
<br><font size=3D2 face=3D"sans-serif"><br>
------<br>
Samuel Toba, Ph.D.<br>
Product Specialist, Catalyst<br>
Rational Drug Design<br>
Accelrys, Inc.<br>
9685 Scranton Road<br>
San Diego, CA 92121-3752<br>
Direct: 858-799-5567<br>
Fax: 858-799-5777<br>
Email: stoba~at~accelrys.com<br>
<br>
Catalyst products:<br>
http://www.accelrys.com/catalyst/<br>
<br>
<br>
<br>
</font>
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