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Can we trust docking results? Sept 2010 IBM Systems and Technology Group releases a white paper with eHiTS and Cell
Oct 2008
EPA's ToxCastTM project will use SimBioSys'
eHiTS as docking engine
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2007
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SimBioSys Newsletter
Fall '09- Winter '10
Holiday Issue
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Dear Colleague,
The Holiday Season is here again, and
as we leave our work places, and
head for various family and friends gatherings - we can pause a little
and reflect on our past year's accomplishments. As I sat down to list
our latest achievements, I realized that many of them are already
documented in our blog which we use to keep in touch with many of you.
You can find there the release of eHiTS 2009.0, a state of the art
docking and screening application that has been the first to be ported
to IBM's Cell B/E processor. Just recently we updated our tools with
the release of eHiTS 2009.1 - an important upgrade version, which fixes
some instability issues, improves the accuracy of docking, and
introduces several new features. With this version, we are at the top
of the performance on the Astex - GOLD validation set as you can read
below. We also confirmed that eHiTS 2009 is a great tool for blind
docking - see it in the Science section of this newsletter. This year
we have also significantly improved our retrosynthetic analysis tool:
ARChem - Route Designer, with a dramatic increase in the available
reaction data sources via our collaboration with Elsevier and Symyx,
better and faster algorithms, and no hassle on-line services. However,
we are most proud of the fact that our tools are now widely
used in the industry and the in academia, this is best showcased by the
success stories of our users. Hopefully many more of these success
stories will come next year.
We wish you Happy Holidays, and look
forward to working with you next
year,
Aniko Simon, PhD
Vice President, SimBioSys Inc.
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Newsletter
Content:
- New product releases
- Science & Technology
- Success stories from our users
- Partnerships
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eHiTS
2009.1
A new release of our family of molecular docking and virtual screening
tools (eHiTS, LASSO, Score, and Tune) came out a few weeks ago. Several
new features were added, and several bugs and instability issues have
been fixed, resulting in greater accuracy, and better performance.
http://www.simbiosys.com/blog/2009/11/27/ehits-20091-is-released/
ARChem
2009.1
A long list of added functionalities, algorithmic improvements, new
system design, improved data handling and more, are included in a fresh
release of ARChem that shows significant advances in computer aided
retrosynthetic analysis.
http://www.simbiosys.com/blog/2009/12/10/archem-20091-is-released/
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Blind
Docking with eHiTS 2009:
With growing interest of users in performing blind docking, we carried
out a preliminary evaluation of eHiTS using a published dataset. The
good results suggest that eHiTS is well equipped for handling this
problem.
http://www.simbiosys.com/blog/2009/12/01/ehits-2009-as-a-blind-docking-tool/
Image
Processing Validation Sets:
A new version of CLiDE is about to be released, which will put the
strong OCR engine behind a contemporary user interface. The
chemical structure extraction capabilities were evaluated on a new set
that has been made available online.
http://www.simbiosys.com/blog/2009/06/15/clide-for-converting-structure-images-to-
structure-files/
Free
Scripts:
A few useful scripts, some related to eHiTS, and some generic, are
available as a small courtesy to the comp chem community.
http://www.simbiosys.com/blog/2009/11/24/useful-scripts-available-as-free-download-
on-the-simbiosys-website/
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3. Success stories from our
users
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A
novel non-peptide BACE1 inhibitor was found using eHiTS as a screening
tool:
http://www.simbiosys.com/blog/2009/11/04/a-novel-bace-1-inhibitor-discovered-using-ehits/
eHiTS
showed good capabilities in separating weak binders from inactive
molecules in an EPA study on estrogenicity:
http://pubs.acs.org/doi/abs/10.1021/tx900135x
SPROUT
Lead-Opt was used to optimize the binding of the active
metabolite of the anti inflammatory drug leflunomide to the target
cavities of the P. falciparum and human dihydroorotate dehydrogenases:
http://pubs.acs.org/doi/abs/10.1021/jm800963t
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Along our strong long lasting relationship with Elsevier
regarding retrosynthetic analysis and availability of data to ARChem,
we established in recent months a partnership with another leader of
the chemical content industry: Symyx:
http://www.simbiosys.com/blog/2009/07/16/simbiosys-and-symyx-team-up-
to-enhance-computer-aided-synthesis-design-capabilities/
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