Similarity searching three-dimensional

Catherine Pepperrell, Three-Dimensional Similarity Searching, Research Studies Press, Taunton, UK, 1994. 

Integration of Three-dimensional Substructure Searching and Molecular Modeling Three-dimensional Similarity Searching... 

Renner, S., Schwab, C.H., Gasteiger, J., and Schneider, G. (2006) Impact of conformational flexibility on three-dimensional similarity searching using... 

It can be seen that the definition of three-dimensional similarity is not a solved problem but rather an area of active research. It is possible that the most appropriate definition will depend on the structures of the molecules investigated and on the property to be compared. Thus, computer programs that perform three-dimensional searches might need to include a variety of definitions of similarity. 

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. 

Thorner, D.A., Willett, P., Weight, P.M., and Taylor, R. Similarity searching in files of three-dimensional chemical structures Representation and searching of molecular electrostatic potentials using field-graphs./. Comput.-Aided Mol. Des. 1997, 3 3, 163-174. 

Muchmore, S. W., Souers, A. J., Akritopoulou-Zanze, I. (2006) The use of three-dimensional shape and electrostatic similarity searching in the identification of a melanin-concentrating hormone receptor 1 antagonist. Chem Biol Drug Des 67, 174-176. 

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