![]()
![]()
Submitted by Bruce Slutsky
The aim of the CINF E-News
is to keep the membership aware of division activities at the recent national
meeting. Perhaps only 10% of the membership attended the
Philadelphia convention. Since people at the meeting couldn’t
attend all the technical sessions and social events, this electronic newsletter
attempts to fill the information gap. I have attempted to
amass the Powerpoint files that were presented. I’d like to
thank the presenters who are willing to share their talks with the entire CINF
membership.
![]()
In 2004 the Division of Chemical Information again was fortunate to receive generous financial support from our sponsors to maintain the high quality of the Division's programming at the National ACS Meeting in Anaheim, to promote communication between members at Welcoming Receptions and to support other divisional activities.
The Division gratefully acknowledges contribution from the following sponsors:
| Platinum Level |
Chemical Abstracts Service MDL Information Systems, Inc. Thomson Scientific |
|---|---|
| Gold
Level |
Wiley
Interscience |
| Silver Level | FIZ CHEMIE
Berlin |
| Bronze Level | Accelrys ACS Publications Division GlaxoSmithKline LIONbioscience LHASA Limited Rusch Consulting Group |
| Contributors | SimBioSys Leadscope Inc. |
![]()
Osman Güner, Chair Elect 2005,
| Patricia Kirkwood, Treasurer 2005-06,
| Terry Wright, Program Chair 2005-06,
| Erja Kajosalo, Program Assistant Chair 2005-06,
| Guenter Grethe, Awards Chair 2006-08. | |
The mission statements of both divisions are similar. CINF is revising its
mission statement to be more inclusive;
| CINF programming strongly supports the inclusiveness toward LABA topics;
| CINF will encourage the LABA membership to become involved in all aspects
of the division, including the corresponding committees. | |
![]()
Presentations given at CINF
symposia have been posted to the CINF website with
express permission granted by the authors who retain the original
copyright. These presentations are for information purposes only
and cannot be further disseminated without the author's prior written
permission.
The Editor thanks the speakers
at the Philadelphia meeting who sent me their Powerpoint files to share their
information with CINF members who could not
attend.
![]()
Lorrin Garson wins The 2005 Herman Skolnik
Award
![]()



![]()
Outreach: service and the public's perception of chemistry
| Education: chemistry teaching as a second career
| The state of the chemistry enterprise, 2015 (looking 10 years into
the future). | |
![]()
![]()
Chemical Abstracts Service
submitted by Eric Shively
CAS HIRES VICE
PRESIDENT OF INFORMATION TECHNOLOGY
Brian Bergner to lead CAS'
Information Technology Initiative

COLUMBUS,
OH, August 16, 2004 - Chemical Abstracts Service (CAS) has appointed Brian
Bergner vice president, information technology. His principal
responsibilities include maintaining and developing the technical infrastructure
to support CAS' extensive worldwide database
building and distribution
operations.
"We are delighted to have attracted Brian Bergner to CAS and
Columbus," said Bob Massie, president of CAS. "He has an extraordinary
track
record of technology leadership in the pharmaceutical industry, one of
our principal customer sectors. Brian brings the skills and experience
that
will help CAS move to the next level of information delivery and
analysis."
Prior to joining CAS, Bergner was director, information
technology, for BASF Corporation and was responsible for all technology
infrastructure
in North and South America. Bergner also is the former
vice president of global infrastructure and site services at Pharmacia
Corporation,
where he was responsible for the overall strategy, direction,
planning and execution of global infrastructure technology. Other
significant
past positions include serving as the vice president, global
infrastructure for Merck and Company, vice president, technology
and
operations, for Warner-Lambert Company and various executive-level
positions at Bristol-Myers Squibb Company.
"I am looking forward to
working with an excellent staff of IT professionals at CAS and am proud to be
associated with an organization
whose information services have become
essential in the work of scientists around the world," said
Bergner.
Bergner holds a bachelor's degree in engineering from Marquette
University and continued his graduate studies at Marquette in
electrical
engineering. He is a recognized expert in strategic planning
and business integration, technology globalization, operational
benchmarking
and cost analysis, and is a frequent presenter on technology
issues to scientific audiences. Bergner also holds two patents and has
authored
numerous publications.
CAS, a division of the American
Chemical Society, is an organization of scientists creating and delivering the
most complete and effective
digital information environment for scientific
research and discovery. CAS provides pathways to published research in the
world's journal and
patent literature - virtually everything relevant to
chemistry plus a wealth of information in the life sciences and a wide range of
other
scientific disciplines, back to the beginning of the twentieth
century. In addition to offering STN in North America, CAS publishes the
print
version of Chemical Abstracts (CA), related publications and CD-ROM
services; operates the CAS Chemical Registry; produces a family of
online
databases; and offers the SciFinder desktop research tool. The CAS Web
site is at http://www.cas.org.
------------------------
![]()
-First n-tier informatics platform expressly
designed to boost R&D productivity in the life sciences-
At Drug
Discovery Technology(r) 2004, Elsevier MDL commenced public demonstrations of
MDL(r) Isentris(tm), the first, fully supported, out-of-the-box, n-tier
discovery informatics platform specifically designed for life sciences
researchers. The successor to MDL(r) ISIS, Isentris is unique in supporting
business process, data, and application integration across chemistry and biology
workflows, as well as a new self-service research model.
"The most
pressing challenge for life sciences R&D today is to improve the quality and
throughput of the drug development pipeline and cost-effectively develop more
successful medicines," said Lars Barfod, president and CEO of Elsevier MDL. "MDL
Isentris helps the life sciences industry meet this challenge by providing a
discovery informatics platform that broadly improves project team efficiency,
saves researchers' time, and lowers costs."
Built on over 25 years of
informatics experience, MDL Isentris brings true integration to the discovery
process and empowers life sciences productivity by providing self-service access
to integrated discovery data, new pioneering methods for reducing data
complexity, a modern research environment supporting integrated discovery
applications, and an open, standards-based platform for application development
and integration.
For researchers and
developers, Isentris incorporates a company's enterprise-wide business processes
that govern how information is collected, stored, used, and shared- helping
global project teams operate with consistent data and unified rules governing
data access and analysis. Isentris consolidates a company's chemical and
biological data from multiple public and proprietary sources-ensuring that
critical information gets to the right researchers in the right format. Isentris
integrates the critical software applications research organizations use to
capture, visualize, analyze, manage, and share data-giving scientists the right
tools to exploit their findings fully. Isentris enables research IT groups to
develop and deliver integrated scientific applications and custom functionality
quickly and cost-effectively-promoting more innovative, productive research and
new return-on-investment opportunities.
"MDL Isentris delivers both
an integration engine and a total workflow solution," said Dr. Seth Pinsky,
senior vice president and chief technology officer of Elsevier MDL. "Isentris
builds upon the latest Microsoft(r) client technology to offer a remarkably
intuitive and flexible interface for scientific users. Because ISIS and Isentris
work together, organizations wishing to improve the integration of their
discovery operations can incorporate Isentris as gradually or as rapidly as they
wish, preserving their current investment in informatics
infrastructure."
The four core components of MDL Isentris are the MDL(r)
Base desktop application supporting a unique task-centric workflow that presents
chemistry and biology data in a single view; the MDL(r) Draw chemical
structure-drawing and -rendering tool; the integrating MDL(r) Core
Interface development environment; and MDL(r) Direct (data cartridges) for
storing, searching, and retrieving molecules and reactions using Oracle(r)
technology.
![]()
![]()
![]()
![]()
![]()
![]()
|
Standard mode |
Closest to Xray |
Best scoring |
|---|---|---|
|
Cases when RMSD < 2.0Å |
100% |
66% |
|
Cases when RMSD < 1.5Å |
86% |
51% |
|
Cases when RMSD < 1.0Å |
56% |
29% |
|
Average RMSD |
0.97 Å |
2.06 Å |
| Average time*: | 5 min / ligand | |
The eHiTS run typically takes 2-8 minutes on a single processor workstation
when the standard parameter set is used (producing the above results). The
program also offers the use of another parameter set providing much faster
processing, intended for preliminary screening of large databases. The eHiTS
program runs about 10-20 times faster when this VHTS parameter set is used, i.e.
typical run time is in the range of 10-20 seconds per ligand on a single CPU.
The following table shows the accuracy results obtained when running the program
with the VHTS parameter set.
Note*: the average time in both cases (standard mode and VHTS mode) was
measured on a single processor Pentim IV, 2.4 GHz Linux PC.
|
Fast VHTS mode |
Closest to Xray |
Best scoring |
|---|---|---|
|
Cases when RMSD < 2.0Å |
70% |
44% |
|
Cases when RMSD < 1.5Å |
46% |
29% |
|
Cases when RMSD < 1.0Å |
25% |
18% |
|
Average RMSD |
1.78 Å |
2.66 Å |
| Average
time*: |
29.75 s / ligand | |
The above table demonstrates that the accuracy loss is about 30% with the gain of 10-20 times speed-up.
SimBioSys seeks collaborations with academic research groups that conduct docking studies. The eHiTS software is offered free of charge for academic institutions under such collaborative agreements.![]()
| Visualizations: Leadscope offers a number of methods for visualizing compound sets, structures, and data including statistical summaries of any groupings performed and histogram and scatterplot matrices of the data. |
| Searching: Techniques for searching compound collections include substructure, similarity, exact structure and the searching of the associated information with Boolean operations. |
| Databases: Along with the integration of a company's proprietary structures and data, Leadscope also provides two databases - known drugs and toxicity. |
![]()
![]()
![]()
David Wild and Dimitris Agrafiotis Join the Indiana University Chemical Informatics Program Faculty
David Wild is teaching
the graduate Chemical Information Technology course at Indiana University’s
School of
Informatics during the fall 2004 semester. Also
Dimitris Agriafiotis has joined us as an adjunct professor of informatics.
Dr. Wild earned his Ph.D. in Chemoinformatics at
Sheffield University, United Kingdom, in 1994. For the last few years, he has
been teaching a chemical informatics course in
the pharmaceutical engineering program at the University of
Michigan. Formerly employed by Pfizer, he
left that company to found and direct his own
company, “Wild Ideas Consulting” ( http://www.wildideasconsulting.com/). Dr.
Wild holds a 0.70 FTE appointment as visiting
assistant professor of chemical informatics this year. Dimitris K. Agrafiotis is Senior Research Fellow and Team
Leader of Molecular Design & Informatics at Johnson
& Johnson Pharmaceutical Research &
Development. He received his Ph.D. in theoretical
organic chemistry from Imperial College, University of
London, in 1988 under the directions of Prof.
Henry Rzepa. In 1994, he moved to 3-Dimensional
Pharmaceuticals where he focused on the development of
intelligent computational tools for combinatorial chemistry and structure-based
drug design, serving as Executive Director of Informatics. Following the
acquisition of 3DP by Johnson & Johnson, he assumed line responsibility for
the computer-assisted drug design, informatics and database groups at the
integrated Exton, Cranbury and Spring House sites. He also oversees the
software and database systems supporting compound and screening logistics, and
directs the development of ABCD, a new global informatics platform for
J&J PRD.
![]()
![]()
![]()