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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
Summer
2007 Issue
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In
this issue of the SimBioSys Quarterly Newsletter:
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eHiTS outperforms Glide in an evaluation by Merck
eHiTS was recently
evaluated on 11
targets of pharmaceutical interest in collaboration with Merck
Research Laboratories. The original study (without eHiTS) was
reported at the Fall ACS in 2006 by Dr. Wendy Cornell et.al., and is
currently under publication. This recent testing of eHiTS on the same
set revealed that eHiTS overall performed very well across those 11
families. In particular, it outperformed all the other programs tested
on the Carbonic Anhydrase I family (pdb code: 1azm) with a RIE(*)
value of 51.8. The eHiTS performance average for the entire test set
was 18.7, which was the highest average amongst all the tested
programs, that included Glide, Fred and Flog. Also the sum of RIE's
over all 11 targets is the highest for eHiTS, as shown in the
chart below.
Note (*). RIE stands for Robust Initial
Enhancement and was proposed as a metric to
evaluate the performance of ranking methods in virtual screening by
Sheridan et al [1], and
recently formulated with an analytical formula by Truchon & Bayly [2].
[ref 1] Protocols
for bridging the peptide to nonpeptide gap in topological similarity
searches.
Sheridan, R.P.; Singh, S.B.; Fluder, E.M.; Kearsley, S.K.
J. Chem. Inf. Comput. Sci. 2001, 41, 1395-1406.
[ref 2] Evaluating
Virtual Screening Methods: Good and Bad Metrics for the "Early
Recognition" Problem.
Jean-François Truchon and Christopher I. Bayly
J. Chem. Inf. Model.; 2007;
47(2) pp 488 - 508; DOI: 10.1021/ci600426e
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Screen 1
million ligands in less then a minute with eHiTS LASSO
LASSO is a novel, conformation
independent, ligand-based screening
method capable of scaffold hopping. The method is based on the
Interacting Surface Point Type (ISPT) defined in eHiTS Scoring
function. Similarity is measured based on the surface properties of
potential ligands, disregarding the 2D topology and the conformation of
the ligands. This "fuzzyness" makes the LASSO descriptor suitable for
scaffold hopping applications.
Recently the SimBioSys team have optimized the
search engine for LASSO. The
new LASSO 7.0 is capable of screening very large databases at
lightening fast speeds. In a recent study, 2 million drug-like ligands
were screened to find thrombin inhibitors in just one minute and 47
seconds.
You can try LASSO
for yourself on the
new LASSO Web-User-Interface. With the web-interface any user from any
computer can run
large screening jobs quickly at just the touch of a mouse.
Apply for a demo
account for LASSO today and SimBioSys will direct you to the new
LASSO Web-Interface.
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ECCC 11 awards sponsored by SimBioSys
SimBioSys, a proud sponsor of the 11th
Electronic Computational Chemistry Conference, congratulates the
following winners of the conference:
*ECCC11 Outstanding e-Presentation Award Winner*
Quantum-chemical
study on the mechanism of irreversible inhibition of HIV-1 protease by
epoxide inhibitors
Authors: Juraj Kóna,1,2,* and Paolo Carloni1
1 International School for Advanced Studies (SISSA) and Democritos
Modeling Center for Research in Atomistic Simulation (INFM), via Beirut
2-4, 34014 Trieste, Italy
2 Institute of Chemistry, Slovak Academy of Sciences, Dúbravska
cesta 9, SK-845 38 Bratislava, Slovak Republic
Presentation can be viewed at either http://www.chemkona.sav.sk/eccc11/
or http://people.sissa.it/~kona/eccc11/
*ECCC11 Outstanding Research Contribution Award Winner*
Tunable Hydrogen
Bonds and LBHBs
Authors: Timm Lankau*, Chin-Hui Yu
Department of Chemistry, National Tsing Hua University,
101 Kuang Fu Road, Section 2, 30013 HsinChu , Taiwan
Presentation can be viewed at http://oxygen.chem.nthu.edu.tw/ECCC11/
We also thank the ECCC11 Scientific Organizing Committee for their help
in judging the presentations.
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Meet SimBioSys
at:
SimBioSys would like to invite you to a docking
and screening with eHiTS & LASSO workshop at the Fall ACS National
Meeting in Boston.
Meet our representatives Dr. Zsolt Zsoldos (CEO), Dr Aniko Simon (VP)
and
and Darryl Reid (Application Scientist) at booth # 619 at the 234th ACS
national meeting, Boston MA, Aug
19-23th, 2007
SimBioSys
will be hosting a series of events
as well as presenting at the Phil Magee Memorial Symposium: QSAR
Reborn. Please join us for the following events:
Conference
presentation:
"Conformation
independent QSAR Descriptor, scaffold hopping with surface
property based eHiTS LASSO"
COMP Session: Phil Magee Memorial Symposium: QSAR Reborn
Time: Sunday, 19 August 2007, 1:30 PM
see abstract
Workshop:
"Ligand-Based
Screening with LASSO & Ligand-Protein Docking with eHiTS: Usage,
Results Analysis and Visualization"
Date: Monday, August 20, 12:30 - 2:30 PM
Room: BCEC, room 102A
>>
Click here to register for this workshop
eHiTS LASSO is a ligand based screening tool that uses the chemical
features on 3D ligand surfaces to create fingerprints for rapid
screening of large databases. eHiTS is an accurate fragment-based
docking program for both virtual screening and binding pose prediction
of ligands. CheVi is an advanced 3D visualization package specifically
designed to help users analyze how ligands interact with receptors. In
addition, CheVi acts as a front-end GUI to run eHiTS LASSO and eHiTS
screening / docking jobs. Participants will get a hands on experience
on how to use all these tools efficiently.
Booth special events:
Using Computer Assisted Organic Synthesis Design in Teaching
Date & Time: Mon., Aug 20, 2007 11:00 - 11:30 am
Location: booth #619
see abstract
Scaffold hopping with a new QSAR descriptor: LASSO
Date & Time: Tue., Aug 21, 2007 11:00 - 11:30 am
Location: booth #619
see abstract
Docking with eHiTS_HS; high performance at low price
Date & Time: Wed., Aug 22, 2007 11:00 - 11:30 am
Location: booth #619
see abstract
SimBioSys will also be participating in a number
of eChemInfo events this year:
Jun 25-29, 2007,
Oxford, UK
Latest Advances in Drug Discovery Design &
Planning Methods
a Hands-on 5 Day eCheminfo Advanced Training Workshop Week
Location:
Chemistry Research Laboratory, Oxford University, Oxford, UK
(registration closed)
Abstracts and Bios
Sep 10-14, 2007,
Oxford, UK
Latest Advances in
Drug Discovery Design & Planning Methods
a Hands-on 5 Day
eCheminfo Advanced Training Workshop Week
Location: Chemistry Research Laboratory, Oxford University, Oxford, UK
Brochure
Abstracts and Bios
Oct 15-19, 2007,. Bryn
Mawr College, Philadelphia, USA
We are presenting at the eCheminfo Community of
Practice meeting at Bryn
Mawr in October. The conference and workshop program is very strong,
and the
meeting has a format designed to support scientific discussion, best
practice
sharing and the development of collaboration opportunities and joint
research
projects. Do consider joining us there:
Latest
Advances in Drug Discovery & Development
15-19 October 2007
Community of Practice Meeting, Autumn 2007
a joint InnovationWell and eCheminfo InterAction Meeting
Bryn Mawr College, Philadelphia
Early registration and reduced rates close on June 30. Potential
registrants
should contact Nicki
Douglas.
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Recent Publications:
Jun 2007,
Frontiers in Drug Design and Discovery,
ISBN: 90-77527-03-6, Volume 3, 2007, Pp. 477-502:
Structure-Based
Virtual Screening
T. Polgár and G.M. Keseru
View: chapter
The
authors give a comprehensive review of structure-based virtual screening,
discuss the theory and the leading edge methodologes used, they also
present a validation study and a study in which the performance of
FlexX, FlexX-Pharm and eHiTS is evaluated on a nuclear receptor. They
concluded that eHiTS without any restrictions on the interactions
outperformed FlexX and FlexX-Pharm.
Jul 2007, Bioorganic &
Medicinal Chemistry Volume 15, Issue 14, 15 July 2007, Pages 4985-5002:
Discovery of
structurally diverse HIV-1 integrase inhibitors based on a chalcone
pharmacophore
Jinxia Deng, Tino Sanchez, Laith Q. Al-Mawsawi, Raveendra Dayam,
Rosendo A. Yunes, Antonio Garofalo, Michael B. Bolgerd and Nouri
Neamati
View: article
doi:10.1016/j.bmc.2007.04.041
The
authors compare eHiTS versus Gold for the discovery of HIV-1 integrase inhibitors and conclude that
"the enriched eHiTS score is the most
efficient index
to distinguish
active over inactive compounds, compared with both the fitting value
and GOLD score."
See full list of user publication with SimBioSys software tools: here
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