[Product Releases]
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[Blog]
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[News]
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IBM's Systems & Technology Group releases a white paper with
eHiTS & Cell
Oct 2008 Virtual Screening by Flexible Docking on a PlayStation 3
Apr, 2008
EPA's ToxCastTM project will use SimBioSys' eHiTS as docking engine
Nov, 2007
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[Events]
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| 239th ACS
Mar 21-25, 2010
San Francisco, CA, USA
Talk #81
see >> more
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Press Releases in 2005:
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Flexible
ligand docking tool eHiTS v5.3 was released
Wed.,Dec 14, 2005:A new version of the
flexible ligand docking tool eHiTS v5.3 was released today!
At SimBioSys Inc. we are pleased to announce
the release of the latest version of our flexible ligand docking tool,
eHiTS 5.3. eHiTS 5.3 is the truly systematic and exhaustive docking
tool that performs docking with no seed bias, automatically detects
binding sites and evaluates all possible protonation states of the
ligand and receptor in a single run.
eHiTS 5.3 has a completely new approach to the
scoring function problem. eHiTS 5.3 uses the temperature factors
included in PDB files to create a set of "statistically derived
empirical scoring functions". The result is a far more accurate docking
algorithm, average results show a 25-30% improvement in the top scoring
pose in terms of RMSD to the x-ray pose. The new scoring function can
be easily trained or tuned using any available data to achieve even
better results.
eHiTS 5.3 also includes a very fast
pre-screening filter tool that can screen 6 ligands per second on a
single CPU PC, making it applicable for large ligand screens. To read
more about what's new in eHiTS v5.3, please visit: http://www.simbiosys.com/ehits/index.html
For more information and to obtain an
evaluation copy please visit www.simbiosys.com
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New
Lead Optimiztion Tool released by SimBioSys and University of Leeds, UK
Tue.,Dec 06, 2005: Optimizing lead drug
candidates is an essential part of any drug discovery program. The
latest release from the SPROUT product line, directly addresses this
important problem. In contrast to it's parent SPROUT, SPROUT-LeadOpt is
not a de novo design system, but rather has been specifically designed
to optimize lead candidates within the boundaries of a receptor site.
It addresses two important aspects of the structure based lead
optimization problem: core extension and monomer replacement.
Core Extension uses a set of synthetic chemistry
rules to identify reactive functional groups in a bound ligand and then
generates extended structures in a combinatorial fashion by carrying
out virtual synthetic chemistry using common synthetic reactions and a
database of monomer structures.
Monomer Replacement uses retrosynthetic
fragmentation to identify monomers within one or more bound ligands.
These monomers are then replaced in combinatorial fashion by
structurally related molecules taken from a monomer library to create
new molecular structures.
In both cases many of the newly generated ligand
structures will have significant improvements in predicted binding
affinities over the original ligand(s), and have the distinct advantage
that synthetic accessibility is assured because synthetic
considerations have been built into the optimization process. Like
SPROUT, SPROUT-LeadOpt contains a full suite of analysis tools to help
rank and sort the results.
Try SPROUT-LeadOpt for FREE!
Apply for an evaluation version of
SPROUT-LeadOpt at www.simbiosys.com
The SimBioSys Team.
About the SPROUT product line:
The SPROUT product line has emerged from the classic de novo design
program, SPROUT. SPROUT has a long history in the pharmaceutical
industry. Continuously developed over the past 15+ years, it contains a
comprehensive suite of modules which address different aspects of the
de novo design problem.
About SimBioSys:
Simulated Biomolecular Systems Inc. is a Toronto based chemistry
software company specializing in drug design and drug discovery
software. Along with the SPROUT product line, for de novo design and
lead optimization, SimBioSys also markets eHiTS, a flexible ligand
docking tool, CAESA, for retrosynthetic analysis of organic molecules,
and CLiDE for chemical structure recognition. For more information
about SimBioSys, please visit our website, www.simbiosys.com
About ICAMS, University of Leeds, UK:
Institute for Computer Applications in Molecular Sciences, was
established in 1990, by Prof. A. Peter Johnson at the Chemistry
Department, University of Leeds, UK. The institute is focused on the
following research areas: de novo design, synthetic accessibility &
retrosynthetic analysis, and chemical structure processing. SPROUT,
CLiDE and CAESA were all developed at ICAMS. The founders of SimBioSys
contributed siginificantly to the research and development of those
products.
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ECCC10
winners selected
Tue.,May 17, 2005: the winners
of the ECCC10 Awards, which recognize outstanding presentations
in the 10th Electronic Computational Chemistry Conference were
announced:
Dear ECCC10 Colleagues and Participants,
It is a pleasure to announce the winners of the ECCC10
Awards, which recognize outstanding presentations
in the 10th Electronic Computational Chemistry Conference.
There are two categories in the ECCC10 Awards:
- Best Multimedia Presentation, for the most
effective
use of multimedia techniques and overall quality of
presentation, and
- Outstanding Scientific Presentation, for
outstanding
scientific content, significance, and originality.
There is one winner in the first category and there are
five winners in the second.
The winner of the ECCC10 Award for Best Multimedia Presentation is:
- Presentation # 49: Automated Docking of
Estrogens, Antiestrogens and
SERMs Into an
Estrogen Receptor Alpha and Beta Isoform Using the PMF Forcefield and
the Lamarckian Genetic Algorithm
by Gert Kiss and Noah W. Allen
The winners of the ECCC10 Award for Outstanding Scientific Presentation
are:
- Presentation # 5. The Application of
Composite Energy Method to n-Butyl
Radical
beta-scission Reaction Kinetic Estimations
by Xiaobo Zheng and Paul Blowers
- Presentation # 8. Study of H-Bonded Cluster
Characteristics of Sub- and
Supercritical
Methanol by Computer Simulations
by Sergey P. Krishtal, Michael G.
Kiselev, Arkadiy M. Kolker, and Anatoly G. Zakharov
- Presentation # 16. Oxygen Diffusion in
Minihemoglobin from Cerebratulus
lacteus ? a
Locally Enhanced Sampling Study
by Slawomir Orlowski and Wieslaw
Nowak
- Presentation # 50. The Electronic Structure
and Intrinsic Redox
Properties of [2Fe-2S]+
Clusters with Tri- and Tetra-Coordinate Iron Sites
by Shuqiang Niu, You-Jun Fu,
Lai-Sheng Wang and Toshiko Ichiye
- Presentation # 55. Development of a TIP5P
Consistent Carbohydrate Force
Field
by Sarah M. Tschampel and Robert J.
Woods
Congratulations to all authors of these presentations!
The winners were selected by a special awards committee
from among the conference organizers and participants.
The software prizes which accompany the awards will
be provided to the winners by Parallel Quantum Systems,
(http://www.pqs-chem.com/), Schrodinger (http://www.schrodinger.com/)
and SimBioSys (http://www.simbiosys.com/). Their contributions
have helped raise participation in the ECCC up to record levels.
I would like to especially thank and recognize Guangyu Sun,
the chair of the awards committee, for organizing the awards
program and chairing the committee. I thank the Awards Committee
for their service to the ECCC.
On behalf of the Awards Committee,
Robert
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Prof. Robert Q. Topper
Chair and Associate Professor at the Department
of Chemistry, Medical Technology and Physics, Monmouth University, West
Long Branch, NJ, USA
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Free
eHiTS for Academic
Institutions
Toronto, Canada, Apr 20, 2005:
SimBioSys, Inc., offers eHiTS 5.1 free for teaching and academic
research!
eHiTS is the truly exhaustive docking program that explores the full
conformational and pose space. The newly released version 5.1 ships
with a fully automated training facility that can tune the scoring
function to
particular receptors or protein families, improving both accuracy and
enrichment results.
eHiTS consistently outperforms other docking tools in validation
comparisons, using publically available datasets, resulting in more
accurate docking poses. In addition, the automated handling of
protonation states produces more accurate screening results for large
databases, where up-front estimation of the protonation states for all
ligand/receptor combinations is impossible. eHiTS evaluates all
possible protonation states in a single run.
To further improve the great results of eHiTS, the new training
facility
allows the user to tailor the scoring functions to recognize particular
families of interest and better score ligands that make key
interactions.
The training utility is very simple to use and can improve both
accuracy and enrichment results.
SimBioSys recognizes the importance of docking research in the academic
world, and the financial constraints of many academic
institutions. With this in mind, we are offering eHiTS 5.1 free
for most academic institutions.
For more information about eHiTS 5.1 and to obtain an evaluation of the
software, please visit our website (www.simbiosys.com) and fill out a
demo
request form.
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SPROUT
6.0 was released:
Toronto, Canada, January 27, 2005:
Announcing SPROUT v6.0 de novo ligand
design software.
The ability to design drugs that bind strongly within a receptor site
has long been a goal of medicinal/computational chemists. The
latest version of the sophisticated program, SPROUT v6.0, brings
chemists closer to that goal. SPROUT v6.0 is a mature de novo ligand
design package that gives users unsurpassed control over the drug
design process, while allowing for automated options. SPROUT v6.0
takes advantage of parallel processing environments to reach
state-of-the-art computational speeds.
SPROUT v6.0 has an impressive list of features:
* Exhaustive and systematic
coverage of the search space
* Excellent visualization
capabilities
* Generic skeletons that
represent all interesting chemical space
* Improved lone pair
directionality
* Complexity analysis for
ranking and pruning structures
* Specific library for
peptide generation
* Plus many, many, more!!
SPROUT v6.0 is highly tuned for Linux and Silicon Graphics IRIX
operating
systems. To receive a free evaluation version of SPROUT v6.0,
please email SimBioSys at info@simbiosys.com or visit our website at
www.simbiosys.com.
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