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338 Database entries



SPROUT


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OS: Linux





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.

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.

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.

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.

de-novo ligand design
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.

Results Interpretation
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.



Link: http://www.simbiosys.ca/sprout/index.html


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