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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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243rd ACS
Mar 25-29, 2012
San Diego, CA
see
>> more
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Products
SimBioSys®
designs and develops computational chemistry software products in the
area of molecular modeling, e.g. software tools for rational drug design. These
software tools
support the design and optimization of small, organic therapeutics both
in cases
when a protein structure is available, and also in cases when only a
pharmacophore model is given, e.g. generated from the overlay of the
'hit' molecules from high throughput screening. Our software products
are distinguished by high quality scientific modeling and accurate
predictions achieved by robust,
deterministic and exhaustive algorithms innovated by SimBioSys.
Such algorithms are unique in the industry for providing guaranteed
success
and optimal solutions for every problem.
The algorithmic advantages of our products are
coupled
with the technological superiority achieved by the use of modern
technological standards, built into our molecular modelling platform MoDeST®
and high quality visualization platform CheVi®.
For high-level info see: SimBioSys Products
Overview Sheet
Dr. Wendy Warr,
Associate Editor, J. Chem. Inf. Model., wrote recently:
"In computer-aided drug design four situations can arise. In the first
case, if the receptor structure is unknown, and there are no known
ligands, computational techniques can be used to design collections of
compounds with diverse structures for high throughput screening (HTS).
In another case, the structure of the target or receptor is known, and
the structure of the ligand is known. In this case protein-docking
algorithms can be used to place candidate compounds within the active
site of the target and rank-order them. In the third situation, the
structure of the receptor is known, but the structure of the ligand is
unknown; de novo design techniques can propose new ligands that are
complementary to the active site. In the final case, where the receptor
structure is unknown, but there are ligands of known structure,
ligand-based drug design is carried out."
At SimBioSys, we provide products for all of those cases - and beyond:
Computer Aided
Drug
Design |
Ligand:
unknown |
Ligand:
KNOWN |
| Receptor:
unknown | library design for HTS,
could utilise our tools like:
| LASSO |
| Receptor:
KNOWN |
SPROUT
CAESA |
eHiTS
Score
Tune |
Orthogonal to all of these, i.e. products that could be used anytime by all chemists are:
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Fully automated, truly exhaustive,
systematic, fast and accurate
flexible ligand docking software that is suitable for screening of
large ligand databases against macromolecule targets with structural
data available.
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FREE for
everyone !
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A 3D visualization tool that has been
specifically
designed to help analyse interactions between receptors and ligands,
providing users with valuable information about how and why a molecule
docks in a particular pose.
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Three products are available as part of the
SPROUT product line: |
- SPROUT Classic: main
purpose is
de-novo structure generation by fragment extention, followed by
connection based on template overlapping.
- SPROUT HitOpt:
optimization of
existing "core" structures by using synthetic rules to extend the
"core" to better fulfil the demands of the cavity (note: it is not
considered as a de novo design package).
Addtional functionality of all three packages include: pocket
detection, target site identification, interaction analysis, fragment
docking, automated ligand building, scoring, ranking, clustering of
results and much more...
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ARChem is a retrosynthetic analysis package, which assist chemists to
find routes from target molecules to readily available starting
materials.
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Computer program to automatically analyse and rank
sets of molecules according to their ease of synthesis. It provides
structural complexity analysis and rapid retrosynthetic analysis with
reaction path information including intermediates.
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CLiDE is the OCR system for chemists, it can
recognize and extract structures, reactions and text from scanned
images of printed chemistry literature.
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Some of the above listed products, that SimBioSys
distributes (namely SPROUT, CLiDE and CAESA) were developed by PhD
students and researchers at the Institute
for
Computer Applications in Molecular Sciences, University of
Leeds,
UK. Some of
those developers are currently employed by SimBioSys.
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