Mathematical modeling and screening of ligand binding sites in protein using the tetrahedral motif method and double-centroid representation

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dc.contributor.advisor Reyes, Vicente
dc.contributor.author Banerjee, Arkanjan
dc.date.accessioned 2012-07-18T19:56:48Z
dc.date.available 2012-07-18T19:56:48Z
dc.date.issued 2012-04
dc.identifier.uri http://hdl.handle.net/1850/15250
dc.description.abstract A pharmacophore consists of the parts of the structure of the ligand that are sufficient to express the biological and pharmacological effects of the ligand. It is usually a substructure of the entire structure of the ligand. Small organic molecules called ligands or metabolites in the cell form complexes with biomolecules (usually proteins) to serve different purposes. The sites at which the ligands bind are known as ligand binding sites, which are essentially "pockets" which have complementary shapes and patterns of charge distribution with the ligands. Sometimes a pocket is induced by the ligand itself. If we study different bound conformations of ligands it is found that they share a specific 3 dimensional pattern that is more or less common and is responsible for its binding and which is complimentary in 3 dimensional geometry and charge distribution pattern with its cognate binding site in the protein. This work studies the three dimensional structure of the consensus ligand binding site for the ligand FMN. A training set for the ligand binding sites was made and a 3D consensus binding site motif was determined for FMN. The FMN system was studied and its binding sites in its respective regulator proteins. The ability to identify ligand binding site by scanning the 3D binding site consensus motif in protein 3D structures is an important step in drug target discovery. Once a pharmacophore template is found it can also be used to design other potential molecules that can bind to it and thus serve as novel drugs. en_US
dc.language.iso en_US en_US
dc.subject DCRR en_US
dc.subject Pharmacophore identification en_US
dc.subject Screening en_US
dc.subject Tetrahedral motif en_US
dc.subject.lcc QP517.L54 B36 2012
dc.subject.lcsh Ligand binding (Biochemistry)--Mathematical models en_US
dc.subject.lcsh Drugs--Structure-activity relationships en_US
dc.title Mathematical modeling and screening of ligand binding sites in protein using the tetrahedral motif method and double-centroid representation en_US
dc.type Thesis en_US
dc.description.college College of Science en_US
dc.description.department Department of Biological Sciences en_US

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