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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
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Overview
SPROUT generates all structures that fit a specified set of
constraints. The constraints are described as a set of target sites - small
regions of space where it is desirable to place an atom to promote some
intermolecular interaction. The structures generated can be further constrained
by a volume, such as a receptor site.
SPROUT provides incredible control; users can set various parameters
and structural limits (size, number of rings, rotatable bonds, template
subset etc.) to reduce the search space to a manageable size. This improves
the efficiency as the structure space is searched exhaustively.
The Sprout Software Tool Kit is an interactive system that can assist
in several stages of the structure-based rational drug design process.
The system is modularized and offers automatic methods for solving a number
of problems in drug design. However, the user maintains control and is
able to guide each module, and if necessary modify its decisions. The tool
kit consists of five modules and a Template Library Manager.
SPROUT functions
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Binding Pocket Identification
Detection of potential binding pockets of protein structures
by detecting clefts in the solvent accessible surface of the protein is
done by the CANGAROO module.
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Target Site Identification
Identification of favorable hydrogen bonding and hydrophobic regions
within a binding pocket is done by the HIPPO module. The hydrogen bonding
sites are directional and are used to define target sites for the position
of potential ligand atoms. HIPPO is also able to recognize covalent
and metal target sites.
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Molecular Fragment Docking
User selection of functional groups that are then docked to the target
sites by the program to form starting fragments for structure generation
is provided by the ELEFANT module.
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Generation of skeletons that satisfy the steric constraints of a binding
pocket by growing spacer fragments from the starting fragments and connecting
the resulting skeletons together is done by the SPIDER module.
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The ALLIGATOR module clusters, sorts and scores the solutions as
an efficient means for evaluating the results. It also substitutes heteroatoms
into the skeletons to generate molecules with complementary electrostatic
properties to the receptor site.
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