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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
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[Events]
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| 243rd ACS
Mar 25-29, 2012
San Diego, CA
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Published in the Special Issue of
Journal
of Molecular Structure: THEOCHEM, Volumes 666-667, 29
December 2003, Pages 659-665
Software tools for structure based rational drug design
Zsolt Zsoldos
SimBioSys Inc., 135 Queen's Plate Drive, Unit 355, Toronto, ON, M9W 6V1
Canada
Abstract:
Scientific advancements during the past two decades have
altered
the way pharmaceutical research produces new bioactive molecules.
Traditional
"trial and error" drug discovery efforts are gradually replaced by
structure
based rational drug design. The structure of target ptroteins is
determined
by various techniques, including X-ray crystallography and NMR.
Computer
aided modelling is used to analyse the biological action of the
proteins
and find small molecule ligands that could interact with the target
structure.
The first generation of the software tools were limited to molecular
dynamics simulations based on simple force field models. More automated
methods, like flexible ligand docking and de novo ligand design
programs have emerged in the 90s. However, most of those software
relied on stochastic algorithms to perform the search, effectively
performing a computerised "trial and error" search.
SimBioSys provides ligand design and docking tools that are systematic,
exhaustive, rely on rational rules, heuristics and dynamic knowledge
bases. The novel algorithms designed and optimised to solve the
specific problems greatly outperform the general random methods. The
presentation will give
a brief overview of the efficient algorithms behind the SPROUT (de novo
ligand design) and eHiTS (flexible ligand docking and virtual high
throughput
screening) software tools. Validation test results will be presented to
demonstrate how effective these tools are in practical drug design
problems
Keywords:
Rational drug design; Ligand docking; de novo Design; VHTS; Scoring
function
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Full
Presentation
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