Subject: Abstracts of Papers at ACS - Modeling@Internet

From: "Osman F. Guner" <[email-masked]>
Date: Wed, 30 Dec 1998 08:29:29 -0800

THURSDAY MORNING 
Section A 
Modelling and Analysis Through the Internet 1
O. Güner, Organizer, Presiding

8:30*68. Internet-based modelling and computational chemistry tools. H. Rzepa 
The rapid, and frequently chaotic progress made over the last five years in
chemical utilisation of the Internet will be reviewed. Three issues in
particular will be addressed in detail; the development of structured
documents
capable of storing and expressing chemical data and semantics, the use of the 
model rather than the image media type as an integral part of chemical
documents, and issues surround the authentication of documents and chemical
objects using digital certificates.

9:30*69. Dissertations from chemistry on the internet. J. Gasteiger, W-D.
Ihlenfeldt, R. Hoellering 
An essential part of academic chemical research is performed by graduate
students. Dissertations therefore offer a wealth of information that, quite
often, only partly and slowly finds its way into publications in scientific
journals. The implementation of dissertations on the internet provides rapid
access to this cornucopia of chemical information. It can be accessed by the
search technology employed for chemical databases such as name, structure, and
substructure searching. Furthermore, the information in dissertations can be
enriched by data derived from computations and modeling. Computer programs can
be linked to dissertations to provide active contents, further enriching the
importance of dissertations.

10:00*70. A structure based drug design degree course delivered on the
internet. C. Burt, P. Murray-Rust, T. Brailsford, C. Edge, C. Richardson, J.
Overington 
The paradigm of Structure-Based Drug Design (SBDD) holds the potential to
increase the efficiency of the drug discovery and development process. 
Unfortunately, the rapid development and highly multidisciplinary nature of
the
process has led to a situation where many staff in the pharmaceutical industry
are ill prepared to exploit effectively these techniques to the full.  The
Internet and the technologies of the World Wide Web (WWW) have revolutionised
the way in which information may be communicated and represent an ideal
platform to deliver courses to "retool" working scientists in new
disciplines. 
The Virtual School of Molecular Sciences (VSMS) at the University of
Nottingham
is at the forefront in establishing virtual collaborative courses and has
launched an Internet Structure-Based Drug Design Course.  An overview of the
course and issues related to the delivery of distance learning courses will be
presented.

10:30*71. Sharing chemical information over the internet. L. R. Patiny 
Creating a common database over the internet on which everybody can easily
contribute is difficult because it requires a lot of management. In order to
circumvent this limitation, we have developed a new web server and client
program allowing research laboratories to submit chemical information (name,
structure, bp, mp, NMR, etc.) automatically and which they still be able to
modify at a later date. This information is directly available to the rest of
the scientific community.
This database, containing the chemical information, can be queried from any
web
browser by substructure (requires JAVA), molecular formula, bp, mp, NMR shift,
infra-red maxima, etc.
During this presentation we will explain the concept behind this new server as
well as show the way it works in practice (submitting and retrieving
information).

11:00*72. Modeling and visualization on the web. M. Hahn
The Web provides an ideal medium for allowing broader access to molecular
modeling and molecular visualization.  A key goal is to provide tools that
non-computational scientists find easy to use.  Ease of use, however, must be
balanced with a level of sophistication such that the tools and the
information
they provide are not perceived as trivial. This talk describes various
approaches towards building such balanced modeling and visualization
environments, and describes our experiences with one such environment, WebLab.

THURSDAY AFTERNOON 
Section A 
Modelling and Analysis Through the Internet 2 
New Advances with Internet Software
O. Güner, Organizer, Presiding

1:30*73. Webtables: computing molecular properties on the web. T. J.
O'Donnell,
C. J. Blankley, C. Humblet 
We have developed a web-based interface to assist in the task of computing and
tabulating molecular properties for large sets of compounds.  Data are
manipulated in the form of a table with each row representing one molecule and
each column representing one type of molecular property.  The table is
presented as an HTML page with GIF depictions of selected structures and text
display of selected data columns.  The major function of Webtables is to
compute new columns of data.  All computations are carried out on a web server
Unix machine with the results returned using standard CGI methods.  Data sets
containing as many as 10,000 compounds are accomodated, although sizes nearer
1000 are more commonly used.  The table may be output as a tab-delimited
file. 
Data are input from a variety of input file types.  We will show typical web
page output for a sample session, list all available molecular property
computations and discuss the underlying CGI scripting and the use of Daylight
toolkit in Web Tables.

2:00*74. Chemmart: one-stop web shopping of structural databases. T. J.
O'Donnell, T. N. Doman 
We have developed a web-based application to assist in the searching of
structural databases.  It allows for exact lookups, sub-structural, neighbor
and SMARTS searches. In addition to searching, ChemMart can perform
computations on input structures, such as clogP, "Pfizer Rule of Five"
estimates, Concord 3-D coordinate generation, and polar surface area
computation.  Input and output is managed on a Web page using standard HTML. 
Structures may be sketched in, read from input files, or located by
compound id
number in the databases.  Output may be saved in local files on the web-client
computer.  All searches and computations are carried out on a web server Unix
machine with the results returned using standard CGI methods.  We will show
typical web page output for a sample session, discuss searching strategies and
molecular property computations and explain the underlying CGI scripting.  We
will discuss the use of the ChemDraw plug-in, the Daylight toolkit, and the
interface to helper applications in ChemMart.

2:30*75. Web-based integration of computational experiments with biological
and
chemical information. A. Shah, D. Huhta, H. Li 
It has long been realized that chemistry research can benefit from the
integration of chemical and biological information with modeling and anlysis
tools.  The information can be accessed from a variety of sources, such as
corporate databases and databases on the Internet.  The most significant
benefit of such integration is that computational analysis capabilities add
value to the integrated access to chemio- and bio-informatics.  Such interface
of informatics and analysis provides us the much needed leverage to convert
"information" into "knowledge."  We will describe a client-server model as
implemented in Gene Explorer and MedChem Explorer programs, in which the
information from computational and information servers is seamlessly
integrated.  Examples will be presented that demonstrates the benefits of such
an integrated Web-based environment.

3:00*76. Extending chimera for collaborative molecular visualization. T. E.
Ferrin, C. Huang, T. Klein 
Chimera is a new, highly extensible computer application for visualizing and
interactively manipulating molecular structures that is under development in
the UCSF Computer Graphics Laboratory. Chimera provides for the addition of
new
functionality through use of a high-level programming language called Python. 
We have used this approach to add a prototype “collaboratory” module to
Chimera
for carrying out interactive three-dimensional studies of molecular structures
among collaborating scientists at distant locations.  With our collaboratory,
multiple scientists can interactively manipulate images of shared, complex
three-dimensional molecular models and interact with one another in the same
way that traditional “face-to-face” collaborative scientific experiences would
provide.  When fully implemented, our collaboratory will not  only facilitate
collaborative research projects, but will provide the capability to establish
interactive training sessions on molecular modeling techniques.

3:30*77. Does the web impact computer-assisted drug design. S. Krystek, W.
Langton
At Bristol-Myers Squibb, Web-based tools have been successfully integrated
into
the process for both structure and ligand based drug design.  Web-based tools
are being utilized in distributed environments for virtual screening, lead
generation processing, compound selection, as well as for data management and
the transfer of information among team members.  A practical example will be
presented detailing the use of Web-based tools in day-to-day activities of
computer-assisted drug design.

--
Osman F. Güner, Ph.D.
Sr.Product Manager,    Rational Drug Design
Molecular Simulations Inc.  (619)799-5341
[email-masked]            http://www.msi.com