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[News]
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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
Nov, 2007
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[Events]
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| 240th ACS
Aug 22-26, 2010
Boston, MA, USA
booth #945
see >> more
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SimBioSys Quarterly Newsletter
Winter
2008 Issue
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In
this issue of the SimBioSys Quarterly Newsletter:
- A
message from our Chief Scientific Officer, Dr. Zsolt Zsoldos
- Over
18 Million Molecules Screened against 40
Targets
- New
eHiTS and LASSO Screening Protocol
- The
Search for Unusual Suspects - BioIT World
Article
- SimBioSys
Enters the Blogosphere
- Publications,
Presentations and User Stories
- SimBioSys Events
for 2008
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1.
Message from Dr. Zsoldos, CSO, SimBioSys
The past
three months
have flown by! So far 2008 has started the way 2007 ended,  exciting and very busy.
Over the past quarter, we have continued
our efforts to develop cutting edge chemistry software while expanding
our efforts to reach out into the computational chemistry
community. We have started a project to make LASSO descriptors
available for all 18+ million structures available in the ChemSpider
database and, in addition, have screened the entire database against 40
receptor targets. The results of this very large cross screening
experiment are now available through the ChemSpider website. I am also
pleased to announce that we have recently entered the blogosphere with
our own SimBioSys Blog. Our blog will hopefully serve as another
way to interact with the drug discovery community, and a way for you to
learn what we are up to. In 2008 we are expanding our travel
schedule to try and interact with as many users as possible. I
would like to invite you to let us know if you will be attending any of
the meetings/conference listed in this newsletter, as we would love to
talk with you.
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2.
Over 18 Million Molecules Screened against 40
Targets
SimBioSys and ChemZoo have teamed up to provide the virtual screening
results for 40 target families on the full ChemSpider Library,
currently containing over 18 million molecules. Using the LASSO
similarity search tool, SimBioSys has screened the ChemSpider database
against all 40 target families from the Database of Useful Decoys (DUD)
dataset. In addition to allowing instant ranking results for your
particular target of interest (retrieving molecules that are likely to
be active for your receptor) this matrix of screening results can be
used to find molecules that have predicted affinity for your target but
low predicted affinity for all other targets. Performing such
searches promises to improve selectivity and can be a guide to reducing
toxicity concerns.
We are now in the process of looking to see what LASSO can and can not
do on such a large set of structures, both its limits and its
successes. In the spirit of crowdsourcing, we encourage you to check it
out and would love to get any and all feedback.
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3.
New eHiTS and LASSO Screening Protocol
Getting the
most out of your computational tools often comes down to proper
usage. At SimBioSys our goal has always been to develop tools
that are easy to use, with simple interfaces and a lot of
automation. However, even though the scripts are simple, as a
user you still need to know the best protocol to get the best
performance.
Over the past three weeks, we have been working on the SAMPL project
(http://sampl.eyesopen.com). SAMPL is a community competition to
test protein and ligand modeling. This work has allowed us to
formalize the "best practices" protocol for screening with eHiTS and
LASSO.
The following graphic illustrates the workflow one should follow when
using eHiTS or LASSO for screening databases. The main idea is
that we should first try to generate the best model possible, using all
available information prior to performing the screen. As with any
modeling approach, testing and validating the model is an essential
step prior to applying the model in a predictive way. Thus, in
this workflow we have a series of "loops" which involve testing and
evaluating the model at that step. Before moving to the next step
you must be satisfied with the results.
More information about this new protocol will be available on our blog
as well as our website. We encourage users to make comments on
this protocol via our blog or through email.
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4.
The Search for Unusual Suspects - BioIT World Article
A recent
article in the February edition of BioIT World, focused on the use of
computational tools to expand the range of core molecular shapes for
lead generation. We recommend taking a look at the article as it
gives a nice overview of the work in scaffold hopping
applications. SimBioSys' LASSO ligand based similarity tool was
mentioned in this article.
Kenneth Foreman, computational chemist at OSI Pharmaceuticals
summarizes the main purpose of these tools:
"The lack of bias in these computational tools can aid in converting
[HTS] hits that have certain undesirable core features into new,
IP-able cores" says Foreman.
Rather than go into any more details here, please take a look at the
article for yourself at the link below.
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5.
SimBioSys Enters the Blogosphere
January 9th, 2008. That's the
date SimBioSys entered the Blogosphere. Building upon our efforts
to connect more and more with the drug discovery community, we have
started our company blog. The blog is designed as another
opportunity for our users and friends to find out what SimBioSys is
doing and, more importantly, enter into a discussion on various
happenings in our field.
Over the coming weeks, we are planning to fill the blog with our ideas
and visions for the future of computational chemistry (at least the
small portion in which we have our fingers). We hope this will
prompt some open and frank discussion. We encourage you to
subscribe to our blog, and please, please, comment!
Recent Blog Postings:
Serious Computing on Gaming Hardware
http://www.simbiosys.com/blog/2008/02/21/
the-next-generation-in-performance-serious-computing-on-gaming-hardware/
Exciting times for LASSO - ChemSpider and Bio-IT World
http://www.simbiosys.com/blog/2008/02/13/
exciting-times-for-lasso-chemspider-and-bio-it-world/
Are you aware of SAMPL?
http://www.simbiosys.com/blog/2008/01/26/are-you-aware-of-sampl/
Roping in your next Scaffold Hop with LASSO
http://www.simbiosys.com/blog/2008/01/22/roping-in-you-next-scaffold-hop-with-lasso/
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6.
Presentations, Publications and User
Stories
Presentations from Research Triangle Park Meetings
Last
November, SimBioSys joined local experts in the Research Triangle
Park area of NC, in a series of meetings discussing virtual screening
and docking. Several of the presentations from the two day event
are available on our website:
SimBioSys
Publications
Darryl
Reid, Bashir
S. Sadjad, Zsolt Zsoldos and Aniko Simon: LASSO - ligand activity by
surface similarity order: a new tool for ligand based virtual
screening, in the Journal of Computer-Aided Molecular Design, Published
online: 18 January 2008.
User
Publications and Presentations
Current
Pharmaceutical Analysis, Volume 4, Number 1, February 2008, ISSN: 1573-4129.
Protein-ligand Docking: A Review of Recent Advances and Future
Perspectives. Montserrat Vaque, Anna Ardevol, Cinta Blade, M. Josepa
Salvado, Mayte Blay, Juan Fernandez-Larrea, Lluis Arola and Gerard
Pujadas
PLoS Computational Biology. 2008 Jan;
[Open Access Research Article] In Silico Elucidation of the Molecular
Mechanism Defining the Adverse Effect of Selective Estrogen Receptor
Modulators. Lei Xie, Jian Wang, Philip E. Bourne. DOI: 10.1371
Structure-based Drug Design: Molecular Docking Studies. Jinxia (Nancy)
Deng, PhD, Postdoctoral Research Associate, University of South
California, School of Pharmacy. Sept
25, 2007.
"Elucidation of Mechanisms of Action of Molecules with Anti-Cancer
Activity Using Molecular Docking." Ines Sousa, Visvaldas Kairys, Jose
M. Padron, Miguel X. Fernandes. 2nd Meeting YBIM (Young Biomedical
Investigators of the Macaronesia), held on November 10-13, 2007 at Lanzarote,
Spain.
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7.
SimBioSys Events for 2008
Meet the
SimBioSys team at the following events.
-
SBS
Conference
April
6-10,
2008
St Louis, MO
-
235th ACS
April
6-10,
2008
New Orleans,
LA
- UK
QSAR Spring meeting
Apr
24, 2008
Windlesham,
Surrey, UK
- BIO-IT
Apr 28 -
30,
2008
Boston, MA
- 8th ICCS
June 1 -
5,
2008
5,
2008 Noordwijkerhout, NL
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For
more information on SimBioSys presence at these events please visit:
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