Databases three-dimensional structure searching

A recently released three-dimensional structure searching system is MACCS-3D, which is designed to be coupled with a MACCS-II database enhanced with three-dimensional structural data. The program uses thousands... 

Inorganic Three-dimensional Structure Databases Molecular Docking and Structure-based Design Protein Data Bank (PDB) A Database of 3D Structural Information of Biological Macromolecules Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Databases Structure Representation Three-dimensional Structure Searching,... 

A similarity measure has three main components the structural representation that is used to characterize the molecules the weighting scheme that is used to differentiate mote important features from less important features and the similarity coefficient that is used to quantify the degree of similarity between pairs of molecules. Of these, the first is probably the most important since the representation that is chosen will control the operations that can be carried out when determining the similarity between a pair of molecules. Traditionally, chemical information systems have stored molecules by means of their 2D chemical structure diagrams but such systems increasingly also include 3D information and this division forms the principal basis for categorizing the various similarity measures that have been described (see Structure Databases and Three-dimensional Structure Searching). 

Protein Design Concepts Protein Modeling Protein Structure Prediction in ID, 2D, and 3D Structural Similarity Measures for Database Searching Structure Databases Three-dimensional Structure Generation Automation Three-dimensional Structure Searching. 

Good A C and J S Mason 1995. Three-Dimensional Structure Database Searches. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry Volume 7. New York, VCH Publishers, pp. 67-117. 

Martin YC, Bures MG, Willett P. Searching databases of three-dimensional structures. In Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry, Vol. 1. New York VCH, 1990. p. 213-63. 

Varady J, Wu X, Fang X, Min J, Hu Z, Levant B, Wang S. Molecular modeling of the three-dimensional structure of dopamine 3 (D3) subtype receptor discovery of novel and potent D3 ligands through a hybrid pharmacophore-and structure-based database searching approach. / Med Chem 2003 46 4377-92. 

Yvonne C. Martin, Mark G. Bures, and Peter Willett, Searching Databases of Three-Dimensional Structures. 

Andrew C. Good and Jonathan S. Mason, Three-Dimensional Structure Database Searches. 

Molecular databases and the associated data banks require the development of a conceptual structure for the information stored about the molecules, descriptive language representing the data, and methods for analysis enabling molecular modeling, similarity searches, classification, visualization, or other uses of the database.320 Currendy, the Protein Data Bank (PDB http 7www.rcsb.org/pdb/) is one of the best known examples of a molecular database. The PDB is a worldwide archive of three-dimensional structural data of biological macromolecules.321 The PDB is a common accentor to many structural databases.322 The success of... 

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