Similarity searching atom mapping

SA-Search (http //bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search) can be used to mine for protein structures and extract structural similarities. The stractural alphabet (SA) allows the compression of 3D conformations into a ID representation using a limited number of prototype conformations to permit the 3D similarity searches. STING Mellennium Suite (SMS) at http //trantor.bioc.columbia.edu/SMS provide analysis and visualization of sequence to structure relationships, such as nature and volume of atomic contacts, relative conservation of amino acids at the specific position and indication of folding essential residues, conformational map, rendering and coloring of the molecule. 

The description above has assumed that the property that is stored at the vertices of the tessellated icosahedron describing a molecule is either the minimal or the radial distance to the molecular surface. However, it is equally possible to store at each vertex any sort of property that can be calculated for that point in 3D space, such as the molecular electrostatic potential. Thus SPERM, like atom-mapping, allows local, property-based 3D similarity searching. 

C. A. Pepperrell, P. Willett, and R. Taylor, Tetrahedron Comput. MethodoL, 3,575 (1990). Implementation and Use of an Atom-Mapping Procedure for Similarity Searching in Databases of 3-D Chemical Structures. 

D. J. Wild and P, Willett,/. Chem. Inf. Comput. Sci., 34,224 (1994). Similarity Searching in Files of Three-Dimensional Chemical Structures Implementation of Atom Mapping on the Distributed Array Processor DAP-610, the MasPar MP-1104 and the Connection Machine CM-200. 

The developers of CASREACT have pubhshed methods of assigning and searching both reaction centres and explicit reaction schemes. At the time of writing its user interface does not allow the assignment of atom mappings or reaction centres. CASREACT also can retrieve false hits where the direction of the arrow is reversed, similar to the limitation in ChemBase. Improvements in its user interface may resolve some of these limitations. 

Once a first electron-density map is obtained, it is interpreted by the crystallographer. In the case of a MIR(AS) map, a complete model of the protein has to be fitted to the electron density. The Ca atoms are placed first (chain tracing), and subsequently the complete main chain and the side chains are built, a process which has become more and more automated in recent years, notably when high resolution data are available. In the case of molecular replacement, the search model needs to be updated to reflect the molecule present in the crystal. The model is usually of a similar protein and the changes involve the substitution of some amino acids, the introduction of insertions and deletions, the modification of some loops, and so on. 

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