Three-dimensional substructure searching

Structural Similarity Measures for Database Searching Structure and Substructure Searching Three-dimensional Structure Searching Topological Indices... 

Sheridan RP, Nilakantan R, Rusinko A, Bauman N, Haraki KS, Venkataraghavan R. 3DSEARCH a system for three-dimensional substructure searching. / Chem Inf Comput Sci 1989 29 255-60. 

Van drie, J.H., Weininger, D., and Martin, Y.C. ALADDIN an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures./. Comput.-Aided Mol. Des. 1998, 3, 225-251. 

The database search process starts with a rapid screening process within which molecules possessing properties required from potential hits are sorted out from those that can be excluded a priori. The screen involves substructure match followed by screens matching three-dimensional pharmacophore features, molecular shapes or exclusion volumes and text constraints (ID properties) if present in the query (through Oracle). All this greatly reduces the number of potential hit compounds in the database. The next step of the search pro-... 

The previous section shows how molecular structures stored in an RDBMS can be made available to client programs that traditionally read molecular structure files. The advantage of storing molecular structures in an RDBMS is that the information can be used from within the database, as well as by external clients. For example, it would be possible to search a table of molecular structures for three-dimensional overlap, much like it might be searched for substructure match. Of course, such search functions need to be written and installed as extensions to an RDBMS, just like the matches functions was done for substructure searches. This section shows some possible ways this might be accomplished. 

Cringean JK, Pepperrell CA, Poirrette AR, Willett P. Selection of screens for three-dimensional substructure searching. Tetrahedron Comput Methodol 1990 3 37 46. 

ALADDIN An Integrated Tool for Computer-Assisted Molecular Design and Pharmacophore Recognition from Geometric, Stetic, and Substructure Searching of Three-Dimensional Molecular Structures. 

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

IV, INTEGRATION OF THREE-DIMENSIONAL SUBSTRUCTURE SEARCHING AND MOLECULAR MODELING... 

Structural Three-dimensional Large units (molecules) Large character set (over 100 different atom and bond symbols Exact or inexact match Whole or part unit match i. e. substructure search) with multidirectional pathtracing 1... 

Brint, A.T. Mitchell, E. Willett, P. Substructure Searching in Files of Three-Dimensional Chemical Structures. In these Proceedings. 

Biological macromolecules present special problems for substructure searching. In many cases the feature of interest is the one-dimensional sequence of amino-acid or nucleotide residues, and a number of databases of such sequences are now available for searching. Searching of the three-dimensional structure of such macromolecules is also of interest. ... 

SUBSTRUCTURE SEARCHING IN FILES OF THREE-DIMENSIONAL CHEMICAL STRUCTURES... 

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