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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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| 243rd ACS
Mar 25-29, 2012
San Diego, CA
see >> more
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SimBioSys Quarterly Newsletter
Fall
2007 Issue
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In
this issue of the SimBioSys Quarterly Newsletter:
- A
message from our Chief Scientific Officer,
Dr. Zsolt Zsoldos
- SimBioSys
Partners with the US Environmental
Protection Agency on a large scale toxicology screening project,
ToxCast
- eHiTS
is the docking program selected by the
FightMalaria@Home project
- Dr.
Piotras Cimmperman releases a graphical
user interface (GUI) for eHiTS convert
- An invitation to
Docking and Screening
workshops in the Research Triangle Park, NC
- Dr.
Antony Williams supports the SimBioSys team
in a consultative role
- User Success
Stories
- BACE-1 Inhibitors
- Antibacterials (aaRS)
- Upcoming Events
for SimBioSys
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1.
Message from Dr. Zsoldos, CSO, SimBioSys
Summer 2007
has, as usual, been a stimulating and exciting few months.
Continuing our ongoing efforts to deliver
solutions to your problems we
have retained our focus on optimizing our present software products
while keeping a keen eye on opportunities for breakthroughs in
technology. Over the past few months SimBioSys has formed a number of
partnerships with leading scientific groups to work on some community
centric projects. In particular, we have formed a relationship with the
US Environmental Protection Agency to provide access to SimBioSys’
eHITS to support their ToxCast project. Also, we are supporting the
FightMalaria@Home project in their efforts to find new desperately
needed therapies for this killer disease. At a personal level I have
been focused on a high impact project capable of delivering enormous
breakthroughs in the timescales associated with virtual screening via
docking. Details will soon be forthcoming but the work performed to
date clearly demonstrates the advantages new hardware can bring to
high-throughput processes without any compromise in accuracy. In the
coming months SimBioSys will be attending and hosting a number of
events and we hope to have the opportunity to meet with you. Finally I
would like to welcome Dr. Antony Williams into the SimBioSys team. Dr.
Williams brings his extensive experience and expertise in the chemistry
software industry and will support us in a consultative role around a
number of our developing opportunities. We look forward to a prosperous
partnership with him.
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2.
SimBioSys
Partners with the US Environmental Protection Agency on a large scale
toxicology screening project, ToxCastTM
The US
Environmental Protection Agency (EPA) launched phase I of their
ToxCastTM project in August of this year. ToxCastTM will
examine how a
diverse array of environmental chemicals such as pesticides can produce
toxic effects and thereby enable EPA to prioritize the use of its
limited testing resources on those chemicals that present the greatest
likelihood of risk to human health and the environment. The EPA will
augment experimental high throughput screening, with computational
chemistry tools including virtual screening experiments using
SimBioSys' eHiTS docking program.
Zsolt Zsoldos, chief technical officer for SimBioSys comments that "The
ToxCastTM Program will allow the EPA to develop the ability
to forecast
toxicity and develop methods of prioritizing chemicals for further
screening and testing. eHiTS should prove invaluable to integrate in
silico and in vitro endeavors by affording the EPA access to industry
leading algorithms for virtual screening via docking procedures. We are
committed to supporting this project to facilitate improvements in the
processes EPA utilizes in the regulation of environmental contaminants
and in enabling matters of public health."
For more information on this partnership see:
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3.
eHiTS
will be the docking program used in the FightMalaria@Home project
The Centre for Synthesis and Chemical Biology at the Royal College of
Surgeons in Ireland, in collaboration with the Computer Architecture and
Grid Research Group at Trinity College Dublin, have teamed up with SimBioSys to help find novel
anti-malarial drugs and the associated target proteins. Following
the path of successful projects like Folding@Home, fightHIV@home, and Africa@home,
FightMalaria@Home will screen very large compound databases against all
known models of Malaria proteins using idle CPU cycles from users
around the world. A customized version of eHiTS has been
developed to support this worthwhile project. For more
information please visit:
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4.
Dr. Piotras
Cimmperman releases a graphical user interface (GUI) for eHiTS convert
Dr. Piotras Cimmperman, from the Institute of Biotechnology, Vilnius,
Lithuania, has published a multi-platform interface for the convert
utility of SimBioSys' eHiTS package. This GUI, which also includes TMA
to PDB converter, is called "TMAconvert" and it available for Windows,
Linux 32bit and Linux 64bit, or you can download the source code. To
get more information or to access this file conversion tool, please
visit Dr. Cimmperman's website:
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5.
Invitation
to Docking and Screening Workshops in the Research Triangle Park,
NC.
SimBioSys would like to invite you to attend one of two Virtual
Screening and Docking seminars to be held November 27th and 28th in the
Research Triangle Park, NC. SimBioSys will join local experts to
discuss the latest advancements in virtual screening and docking and
exciting new directions for the field.
Tuesday, Nov. 27th ,
2007
School of Social Work, UNC, Chapel Hill
Speakers: Nikolay Dokholyan
(UNC Chapel Hill), Alex Tropsha (UNC
Chapel
Hill), Antonius M Vandongen
(Duke University), Zsolt Zsoldos (SimBioSys)
Hands-on: eHiTS, LASSO and CheVi training session in the afternoon.
Wednesday, Nov.
28th, 2007
NISS 19 T.W. Alexander Drive, Research Triangle Park
Speakers: Rocky Goldsmith
(Environmental Protection Agency), Stan
Young (National Institute of Statistical
Sciences/NCSU), Darryl Reid (SimBioSys),
Zsolt Zsoldos
(SimBioSys)
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6.
Dr.
Antony Williams supports the SimBioSys team
SimBioSys is pleased to welcome Dr. Antony Williams to the team in a
consultative role. Dr. Williams has worked in the
chemistry software field for well over a decade. He brings his vast
knowledge of the field and his desire to solve problems via
cheminformatics software to assist SimBioSys in some new ventures.
Information regarding some of these efforts will be forthcoming and we
look forward to a long and fruitful relationship with Antony.
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7. User
Success Stories
BACE-1 and Novel Antibacterial leads discovered
Two success stories have recently come out of the Fishwick group at the
University of Leeds, UK. In two recent poster presentations,
group members have presented a very successful workflow used to find new BACE-1 inhibitors
as well as Antibacterial leads. The group screens their library
of commercially available compounds against their target using eHiTS
(VHTS mode) then selects roughly 1000 best scoring compounds to
re-score with the SPROUT scoring function. The top 100 then
undergo the “eye” scoring function (they actually look at the compounds
and assess solubility, analog synthesizability etc in order to decide
which ones to purchase for testing in assays. In the BACE-1
project they found 1 active compound out of the 6 tested, while in the
aaRS Antibacterial study they found 8 hits in the 23 tested
compounds.
You can read these success stories and other user publications under
the “Scientific Presentations” page:
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8.
Upcoming Events
Meet the SimBioSys team at the following events.
SimBioSys Fall '07 Newsletter
-
Virtual Screening and Docking workshops
Nov 27-28, 2007
Research Triangle Park, NC
-
Virtual Discovery 2008
Jan 23 - 24, 2008
Palm Springs, CA
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-
SBS Conference
April 6-10, 2008
St Louis, MO
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235th ACS
April 6-10, 2008
New Orleans, LA
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Our events
list
is constantly changing and to keep up to date on our events please
visit our website:
http://www.simbiosys.com/whatsnew/index.html
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